diff --git a/src/claude_code_transcripts/__init__.py b/src/claude_code_transcripts/__init__.py
index 33c322d..f2246a2 100644
--- a/src/claude_code_transcripts/__init__.py
+++ b/src/claude_code_transcripts/__init__.py
@@ -1048,6 +1048,7 @@ def render_message(log_type, message_json, timestamp):
 """
 
 # JavaScript to fix relative URLs when served via gisthost.github.io or gistpreview.github.io
+# Fixes issue #26: Pagination links broken on gisthost.github.io
 GIST_PREVIEW_JS = r"""
 (function() {
     var hostname = window.location.hostname;
@@ -1056,17 +1057,63 @@ def render_message(log_type, message_json, timestamp):
     var match = window.location.search.match(/^\?([^/]+)/);
     if (!match) return;
     var gistId = match[1];
-    document.querySelectorAll('a[href]').forEach(function(link) {
-        var href = link.getAttribute('href');
-        // Skip external links and anchors
-        if (href.startsWith('http') || href.startsWith('#') || href.startsWith('//')) return;
-        // Handle anchor in relative URL (e.g., page-001.html#msg-123)
-        var parts = href.split('#');
-        var filename = parts[0];
-        var anchor = parts.length > 1 ? '#' + parts[1] : '';
-        link.setAttribute('href', '?' + gistId + '/' + filename + anchor);
+
+    function rewriteLinks(root) {
+        (root || document).querySelectorAll('a[href]').forEach(function(link) {
+            var href = link.getAttribute('href');
+            // Skip already-rewritten links (issue #26 fix)
+            if (href.startsWith('?')) return;
+            // Skip external links and anchors
+            if (href.startsWith('http') || href.startsWith('#') || href.startsWith('//')) return;
+            // Handle anchor in relative URL (e.g., page-001.html#msg-123)
+            var parts = href.split('#');
+            var filename = parts[0];
+            var anchor = parts.length > 1 ? '#' + parts[1] : '';
+            link.setAttribute('href', '?' + gistId + '/' + filename + anchor);
+        });
+    }
+
+    // Run immediately
+    rewriteLinks();
+
+    // Also run on DOMContentLoaded in case DOM isn't ready yet
+    if (document.readyState === 'loading') {
+        document.addEventListener('DOMContentLoaded', function() { rewriteLinks(); });
+    }
+
+    // Use MutationObserver to catch dynamically added content
+    // gistpreview.github.io may add content after initial load
+    var observer = new MutationObserver(function(mutations) {
+        mutations.forEach(function(mutation) {
+            mutation.addedNodes.forEach(function(node) {
+                if (node.nodeType === 1) { // Element node
+                    rewriteLinks(node);
+                    // Also check if the node itself is a link
+                    if (node.tagName === 'A' && node.getAttribute('href')) {
+                        var href = node.getAttribute('href');
+                        if (!href.startsWith('?') && !href.startsWith('http') &&
+                            !href.startsWith('#') && !href.startsWith('//')) {
+                            var parts = href.split('#');
+                            var filename = parts[0];
+                            var anchor = parts.length > 1 ? '#' + parts[1] : '';
+                            node.setAttribute('href', '?' + gistId + '/' + filename + anchor);
+                        }
+                    }
+                }
+            });
+        });
     });
 
+    // Start observing once body exists
+    function startObserving() {
+        if (document.body) {
+            observer.observe(document.body, { childList: true, subtree: true });
+        } else {
+            setTimeout(startObserving, 10);
+        }
+    }
+    startObserving();
+
     // Handle fragment navigation after dynamic content loads
     // gisthost.github.io/gistpreview.github.io loads content dynamically, so the browser's
     // native fragment navigation fails because the element doesn't exist yet
@@ -1085,7 +1132,7 @@ def render_message(log_type, message_json, timestamp):
     // Try immediately in case content is already loaded
     if (!scrollToFragment()) {
         // Retry with increasing delays to handle dynamic content loading
-        var delays = [100, 300, 500, 1000];
+        var delays = [100, 300, 500, 1000, 2000];
         delays.forEach(function(delay) {
             setTimeout(scrollToFragment, delay);
         });
diff --git a/tests/test_generate_html.py b/tests/test_generate_html.py
index 2fa6e03..32120c5 100644
--- a/tests/test_generate_html.py
+++ b/tests/test_generate_html.py
@@ -466,6 +466,43 @@ def test_handles_empty_directory(self, output_dir):
         inject_gist_preview_js(output_dir)
         # Should complete without error
 
+    def test_gist_preview_js_skips_already_rewritten_links(self):
+        """Test that GIST_PREVIEW_JS skips links that have already been rewritten.
+
+        When navigating between pages on gistpreview.github.io, the JS may run
+        multiple times. Links that have already been rewritten to the
+        ?GIST_ID/filename.html format should be skipped to avoid double-rewriting.
+
+        This fixes issue #26 where pagination links break on later pages.
+        """
+        # The JS should check if href already starts with '?'
+        assert "href.startsWith('?')" in GIST_PREVIEW_JS
+
+    def test_gist_preview_js_uses_mutation_observer(self):
+        """Test that GIST_PREVIEW_JS uses MutationObserver for dynamic content.
+
+        gistpreview.github.io loads content dynamically. When navigating between
+        pages via SPA-style navigation, new content is inserted without a full
+        page reload. The JS needs to use MutationObserver to detect and rewrite
+        links in dynamically added content.
+
+        This fixes issue #26 where pagination links break on later pages.
+        """
+        # The JS should use MutationObserver
+        assert "MutationObserver" in GIST_PREVIEW_JS
+
+    def test_gist_preview_js_runs_on_dom_content_loaded(self):
+        """Test that GIST_PREVIEW_JS runs on DOMContentLoaded.
+
+        The script is injected at the end of the body, but in some cases
+        (especially on gistpreview.github.io), the DOM might not be fully ready
+        when the script runs. We should also run on DOMContentLoaded as a fallback.
+
+        This fixes issue #26 where pagination links break on later pages.
+        """
+        # The JS should listen for DOMContentLoaded
+        assert "DOMContentLoaded" in GIST_PREVIEW_JS
+
 
 class TestCreateGist:
     """Tests for the create_gist function."""