diff --git a/src/htmlminifier.js b/src/htmlminifier.js
index 2a6f3f73..92dec1bf 100644
--- a/src/htmlminifier.js
+++ b/src/htmlminifier.js
@@ -888,7 +888,9 @@ function minify(value, options, partialMarkup) {
       }
       var token = uidAttr + ignoredCustomMarkupChunks.length;
       ignoredCustomMarkupChunks.push(match);
-      return '\t' + token + '\t';
+      var prefix = /^\s*\n/.test(match) ? '\n' : '\t';
+      var postfix = /\n\s*$/.test(match) ? '\n' : '\t';
+      return prefix + token + postfix;
     });
   }
 
diff --git a/tests/minifier.js b/tests/minifier.js
index 61c8ec2f..c6988f32 100644
--- a/tests/minifier.js
+++ b/tests/minifier.js
@@ -1633,6 +1633,13 @@ QUnit.test('Ignore custom fragments', function(assert) {
     ignoreCustomFragments: reFragments
   }), output);
 
+  input = '<script>//\r\n<% ... %></script>';
+  output = '<script>\r\n<% ... %></script>';
+  assert.equal(minify(input, {
+    minifyJS: true,
+    ignoreCustomFragments: reFragments,
+  }), output);
+
   input = '{{ if foo? }}\r\n  <div class="bar">\r\n    ...\r\n  </div>\r\n{{ end \n}}';
   output = '{{ if foo? }}<div class="bar">...</div>{{ end }}';
   assert.equal(minify(input, {}), input);