diff --git a/src/Microsoft.ML.Tokenizers/Utils/BytePairEncoder.cs b/src/Microsoft.ML.Tokenizers/Utils/BytePairEncoder.cs
index 725eafa002..9e8a45d4ea 100644
--- a/src/Microsoft.ML.Tokenizers/Utils/BytePairEncoder.cs
+++ b/src/Microsoft.ML.Tokenizers/Utils/BytePairEncoder.cs
@@ -20,6 +20,15 @@ public static (int Id, int TokenIndex, int TokenLength)[] BytePairEncode(ReadOnl
                 return [(ranks[mergingBytes], 0, 1)];
             }
 
+            // For large inputs, use heap-based algorithm to avoid O(n²) behavior.
+            // Threshold of 128 chosen empirically: linear scan is cache-friendly for small inputs,
+            // while heap overhead (O(log n) per operation) becomes worthwhile for larger inputs.
+            // Based on upstream tiktoken using 100, adjusted upward for C#'s efficient span operations.
+            if (mergingBytes.Length > 128)
+            {
+                return BytePairEncodeLarge(mergingBytes, ranks, indexMappingSpan);
+            }
+
             (int Index, int Rank)[]? arrayPoolArray = null;
             int requiredLength = mergingBytes.Length + 1;
             Span<(int Index, int Rank)> byteIndicesAndRanks = requiredLength <= 64 ?
@@ -116,6 +125,168 @@ int GetRank(Span<(int Index, int Rank)> byteIndicesAndRanks, int startIndex, int
             return result;
         }
 
+        private struct State
+        {
+            public int Prev;
+            public int End;
+            public int NextEnd;
+            public int NextRank;
+            // Note: In the Tiktoken tokenizer, the rank is also the token Id.
+            // This field is used to cache the rank/Id after a merge so we don't need to re-look it up.
+            // Using this code with a different tokenizer where rank != token Id would produce wrong results.
+            public int CurRank;
+        }
+
+        private struct MergeEntry : IComparable<MergeEntry>
+        {
+            public int Rank;
+            public int Start;
+
+            public int CompareTo(MergeEntry other)
+            {
+                int rankComparison = Rank.CompareTo(other.Rank);
+                if (rankComparison != 0)
+                {
+                    return rankComparison;
+                }
+                return Start.CompareTo(other.Start);
+            }
+        }
+
+        private static (int Id, int TokenIndex, int TokenLength)[] BytePairEncodeLarge(ReadOnlyMemory<byte> mergingBytes, IReadOnlyDictionary<ReadOnlyMemory<byte>, int> ranks, ReadOnlySpan<int> indexMappingSpan)
+        {
+            int stateLength = mergingBytes.Length;
+            State[] statePoolArray = ArrayPool<State>.Shared.Rent(stateLength);
+            Span<State> state = statePoolArray.AsSpan(0, stateLength);
+
+            state[0] = new State
+            {
+                Prev = int.MaxValue,
+                End = 1,
+                NextEnd = 2,
+                NextRank = int.MaxValue,
+                CurRank = int.MaxValue
+            };
+
+            var heap = new PriorityQueue<MergeEntry>();
+
+            for (int i = 0; i < mergingBytes.Length - 1; i++)
+            {
+                var slice = mergingBytes.Slice(i, 2);
+                if (ranks.TryGetValue(slice, out int rank))
+                {
+                    heap.Enqueue(new MergeEntry { Start = i, Rank = rank });
+                    state[i].NextRank = rank;
+                }
+
+                state[i + 1] = new State
+                {
+                    Prev = i,
+                    End = i + 2,
+                    NextEnd = i + 3,
+                    NextRank = int.MaxValue,
+                    CurRank = int.MaxValue
+                };
+            }
+
+            // Local function to add a potential merge to the heap.
+            void PotentialMerge(Span<State> stateSpan, PriorityQueue<MergeEntry> heapQueue, int start, int nextEndItem)
+            {
+                stateSpan[start].NextEnd = nextEndItem;
+                stateSpan[start].NextRank = int.MaxValue;
+
+                if (nextEndItem <= mergingBytes.Length)
+                {
+                    var slice = mergingBytes.Slice(start, nextEndItem - start);
+                    if (ranks.TryGetValue(slice, out int rank))
+                    {
+                        heapQueue.Enqueue(new MergeEntry { Start = start, Rank = rank });
+                        stateSpan[start].NextRank = rank;
+                    }
+                }
+            }
+
+            while (heap.Count > 0)
+            {
+                MergeEntry left = heap.Dequeue();
+
+                if (left.Rank == int.MaxValue)
+                {
+                    break;
+                }
+
+                if (left.Rank != state[left.Start].NextRank)
+                {
+                    continue;
+                }
+
+                int leftStart = left.Start;
+                int rightStart = state[leftStart].End;
+                int rightEnd = state[leftStart].NextEnd;
+                int rightNextEnd = state[rightStart].NextEnd;
+
+                state[leftStart].CurRank = state[leftStart].NextRank;
+                state[leftStart].End = rightEnd;
+                PotentialMerge(state, heap, leftStart, rightNextEnd);
+
+                if (rightEnd < state.Length)
+                {
+                    state[rightEnd].Prev = leftStart;
+                }
+
+                if (leftStart > 0)
+                {
+                    int prevStart = state[leftStart].Prev;
+                    PotentialMerge(state, heap, prevStart, rightEnd);
+                }
+
+                state[rightStart].NextRank = int.MaxValue;
+            }
+
+            // Use ArrayPool for the result buffer to avoid List<T> overhead.
+            // The maximum number of tokens is mergingBytes.Length (no merges).
+            var resultPoolArray = ArrayPool<(int Id, int TokenIndex, int TokenLength)>.Shared.Rent(mergingBytes.Length);
+            int resultCount = 0;
+            int currentIndex = 0;
+
+            while (currentIndex < state.Length)
+            {
+                int startIndex = currentIndex;
+                int endIndex = state[currentIndex].End;
+
+                int mappedStartIndex = indexMappingSpan[startIndex];
+                int mappedEndIndex = indexMappingSpan[endIndex];
+
+                int finalEndIndex = endIndex;
+
+                // Handle partial characters/elements at token boundaries.
+                // If the byte at endIndex-1 maps to the same character as endIndex,
+                // extend the token to include the complete character.
+                if (finalEndIndex > 0 && indexMappingSpan[finalEndIndex - 1] == mappedEndIndex)
+                {
+                    finalEndIndex++;
+                    while (finalEndIndex < indexMappingSpan.Length && indexMappingSpan[finalEndIndex] == mappedEndIndex)
+                    {
+                        finalEndIndex++;
+                    }
+                }
+
+                int tokenId = state[currentIndex].CurRank != int.MaxValue
+                    ? state[currentIndex].CurRank
+                    : ranks[mergingBytes.SliceStartEnd(startIndex, endIndex)];
+
+                resultPoolArray[resultCount++] = (tokenId, mappedStartIndex, indexMappingSpan[finalEndIndex] - mappedStartIndex);
+
+                currentIndex = state[currentIndex].End;
+            }
+
+            ArrayPool<State>.Shared.Return(statePoolArray);
+
+            var result = resultPoolArray.AsSpan(0, resultCount).ToArray();
+            ArrayPool<(int Id, int TokenIndex, int TokenLength)>.Shared.Return(resultPoolArray);
+            return result;
+        }
+
         private static ReadOnlyMemory<byte> SliceStartEnd(this ReadOnlyMemory<byte> memory, int start, int end) => memory.Slice(start, end - start);
     }
 }
diff --git a/src/Microsoft.ML.Tokenizers/Utils/PriorityQueue.cs b/src/Microsoft.ML.Tokenizers/Utils/PriorityQueue.cs
index 751ce6bc10..5ae1da0cba 100644
--- a/src/Microsoft.ML.Tokenizers/Utils/PriorityQueue.cs
+++ b/src/Microsoft.ML.Tokenizers/Utils/PriorityQueue.cs
@@ -12,6 +12,10 @@ internal class PriorityQueue<T> where T : IComparable<T>
     {
         private readonly List<T> _data;
 
+        public PriorityQueue() : this(0)
+        {
+        }
+
         public PriorityQueue(int capacity)
         {
             _data = new List<T>(capacity);
diff --git a/test/Microsoft.ML.Tokenizers.Tests/TiktokenTests.cs b/test/Microsoft.ML.Tokenizers.Tests/TiktokenTests.cs
index c7c1e342d8..d15ff22aaa 100644
--- a/test/Microsoft.ML.Tokenizers.Tests/TiktokenTests.cs
+++ b/test/Microsoft.ML.Tokenizers.Tests/TiktokenTests.cs
@@ -2,7 +2,6 @@
 // The .NET Foundation licenses this file to you under the MIT license.
 // See the LICENSE file in the project root for more information.
 
-using Microsoft.DotNet.RemoteExecutor;
 using System;
 using System.Buffers;
 using System.Collections.Generic;
@@ -13,6 +12,7 @@
 using System.Text;
 using System.Text.Json;
 using System.Threading.Tasks;
+using Microsoft.DotNet.RemoteExecutor;
 using Xunit;
 
 namespace Microsoft.ML.Tokenizers.Tests
@@ -848,6 +848,76 @@ public void TestOss()
 
         private static IReadOnlyDictionary<string, int>? GetVocabulary(TiktokenTokenizer tiktoken)
             => typeof(TiktokenTokenizer).GetProperty("Vocabulary", BindingFlags.Instance | BindingFlags.NonPublic)?.GetValue(tiktoken) as IReadOnlyDictionary<string, int>;
+
+        [Fact]
+        public void TestLargeInputOptimization()
+        {
+            // Verify that large inputs (>128 bytes) and boundary cases round-trip correctly via the public API.
+            // This exercises the large-input optimization path but does not directly compare it to the small-input path.
+
+            // Test with repeated characters - this is the adversarial case that caused O(n^2) behavior
+            string largeRepeatedInput = new string('a', 1000);
+            IReadOnlyList<int> ids = GPT4.EncodeToIds(largeRepeatedInput);
+            string decoded = GPT4.Decode(ids);
+            Assert.Equal(largeRepeatedInput, decoded);
+
+            // Test with a more realistic large input
+            string largeMixedInput = string.Join(" ", Enumerable.Repeat("Hello World! This is a test.", 50));
+            IReadOnlyList<int> mixedIds = GPT4.EncodeToIds(largeMixedInput);
+            string mixedDecoded = GPT4.Decode(mixedIds);
+            Assert.Equal(largeMixedInput, mixedDecoded);
+
+            // Test boundary case - exactly at threshold (128)
+            string boundaryInput = new string('x', 128);
+            IReadOnlyList<int> boundaryIds = GPT4.EncodeToIds(boundaryInput);
+            string boundaryDecoded = GPT4.Decode(boundaryIds);
+            Assert.Equal(boundaryInput, boundaryDecoded);
+
+            // Test just below threshold (127)
+            string belowThresholdInput = new string('x', 127);
+            IReadOnlyList<int> belowIds = GPT4.EncodeToIds(belowThresholdInput);
+            string belowDecoded = GPT4.Decode(belowIds);
+            Assert.Equal(belowThresholdInput, belowDecoded);
+
+            // Test just above threshold (129)
+            string aboveThresholdInput = new string('x', 129);
+            IReadOnlyList<int> aboveIds = GPT4.EncodeToIds(aboveThresholdInput);
+            string aboveDecoded = GPT4.Decode(aboveIds);
+            Assert.Equal(aboveThresholdInput, aboveDecoded);
+        }
+
+        [Theory]
+        [InlineData(200)]
+        [InlineData(500)]
+        [InlineData(1000)]
+        [InlineData(2000)]
+        public void TestLargeInputConsistency(int length)
+        {
+            // Verify that large inputs are handled correctly by the public API and round-trip successfully.
+            // These tests focus on observable behavior (round-tripping and reconstruction), not on comparing internal code paths.
+
+            // Test with repeated character
+            string inputRepeated = new string('z', length);
+            IReadOnlyList<int> idsRepeated = GPT4.EncodeToIds(inputRepeated);
+
+            // Verify round-trip
+            string decodedRepeated = GPT4.Decode(idsRepeated);
+            Assert.Equal(inputRepeated, decodedRepeated);
+
+            // Test with mixed content (more realistic scenario)
+            string inputMixed = string.Join(" ", Enumerable.Repeat("Hello World! Test123", length / 20 + 1)).Substring(0, length);
+            IReadOnlyList<int> idsMixed = GPT4.EncodeToIds(inputMixed);
+            string decodedMixed = GPT4.Decode(idsMixed);
+            Assert.Equal(inputMixed, decodedMixed);
+
+            // Verify with EncodingToTokens as well
+            IReadOnlyList<EncodedToken> tokens = GPT4.EncodeToTokens(inputRepeated, out string? normalizedText);
+            Assert.Null(normalizedText); // No normalization expected
+
+            // Reconstruct from tokens
+            var reconstructed = string.Concat(tokens.Select(t => t.Value));
+            Assert.Equal(inputRepeated, reconstructed);
+        }
     }
 }