diff --git a/eng/testing/select-affected-tests.cs b/eng/testing/select-affected-tests.cs
index 3a1d52026..9d0f41964 100644
--- a/eng/testing/select-affected-tests.cs
+++ b/eng/testing/select-affected-tests.cs
@@ -679,6 +679,7 @@ private static async Task<List<string>> ChangedFilesAsync(string repoRoot, strin
 
         var packageIds = new HashSet<string>(StringComparer.Ordinal);
         var uncertain = false;
+        var inComment = false;
 
         foreach (var rawLine in output.Split('\n', StringSplitOptions.TrimEntries))
         {
@@ -698,11 +699,52 @@ private static async Task<List<string>> ChangedFilesAsync(string repoRoot, strin
             }
 
             var line = rawLine[1..].Trim();
-            if (string.IsNullOrEmpty(line) || line.StartsWith("<!--", StringComparison.Ordinal))
+            if (string.IsNullOrEmpty(line))
             {
                 continue;
             }
 
+            // Track multi-line XML comment state so that continuation lines
+            // of a block comment don't incorrectly trigger uncertain = true.
+            if (inComment)
+            {
+                var commentEnd = line.IndexOf("-->", StringComparison.Ordinal);
+                if (commentEnd >= 0)
+                {
+                    inComment = false;
+
+                    // Process any content after the comment close marker on the same line.
+                    line = line[(commentEnd + 3)..].Trim();
+                    if (string.IsNullOrEmpty(line))
+                    {
+                        continue;
+                    }
+                }
+                else
+                {
+                    continue;
+                }
+            }
+
+            var commentStart = line.IndexOf("<!--", StringComparison.Ordinal);
+            if (commentStart >= 0)
+            {
+                // If the comment doesn't close on this line, enter multi-line comment mode.
+                if (line.IndexOf("-->", commentStart + 4, StringComparison.Ordinal) < 0)
+                {
+                    inComment = true;
+                }
+
+                if (commentStart == 0)
+                {
+                    // Entire line is a comment — skip it.
+                    continue;
+                }
+
+                // Content precedes the comment; trim off the comment (and anything after it) before further processing.
+                line = line[..commentStart].Trim();
+            }
+
             if (line.Contains("PackageVersion", StringComparison.Ordinal) &&
                 TryGetAttributeValue(line, "Include", out var include))
             {
@@ -710,7 +752,10 @@ private static async Task<List<string>> ChangedFilesAsync(string repoRoot, strin
                 continue;
             }
 
-            uncertain = true;
+            if (!string.IsNullOrEmpty(line))
+            {
+                uncertain = true;
+            }
         }
 
         return (packageIds, uncertain);