diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 08ef7a8213..d3c95a456d 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -230,7 +230,8 @@ only faster.")
               (sha256
                (base32
                 "0i99wf9xd3hw1sj2sazychb9prx8nadxh2clgvk3zlmb28v0jbfz"))
-              (patches (search-patches "classpath-aarch64-support.patch"))))
+              (patches (search-patches "classpath-aarch64-support.patch"
+                                       "classpath-miscompilation.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -247,17 +248,6 @@ only faster.")
              "--disable-gjdoc")
        #:phases
        (modify-phases %standard-phases
-         ;; XXX: This introduces a memory leak as we remove a call to free up
-         ;; memory for the file name string.  This was necessary because of a
-         ;; runtime error that would have prevented us from building
-         ;; ant-bootstrap later.  See https://issues.guix.gnu.org/issue/36685
-         ;; for the gnarly details.
-         (add-after 'unpack 'remove-call-to-free
-           (lambda _
-             (substitute* "native/jni/java-io/java_io_VMFile.c"
-               (("result = cpio_isFileExists.*" m)
-                (string-append m "\n//")))
-             #t))
          (add-after 'install 'install-data
            (lambda _ (invoke "make" "install-data"))))))
     (native-inputs
diff --git a/gnu/packages/patches/classpath-miscompilation.patch b/gnu/packages/patches/classpath-miscompilation.patch
new file mode 100644
index 0000000000..835113df71
--- /dev/null
+++ b/gnu/packages/patches/classpath-miscompilation.patch
@@ -0,0 +1,31 @@
+For some reason, the original code gets miscompiled on x86_64, leading
+'Java_java_io_VMFile_isFile' to return true when the return value of
+'cpio_checkType' is ENOENT (= 2).
+
+See <https://issues.guix.gnu.org/issue/36685>
+and <https://issues.guix.gnu.org/49990>.
+
+diff --git a/native/jni/java-io/java_io_VMFile.c b/native/jni/java-io/java_io_VMFile.c
+index de1320b..9a5d375 100644
+--- a/native/jni/java-io/java_io_VMFile.c
++++ b/native/jni/java-io/java_io_VMFile.c
+@@ -278,6 +278,7 @@ Java_java_io_VMFile_isFile (JNIEnv * env,
+   const char *filename;
+   int result;
+   jint entryType;
++  jboolean isfile;
+ 
+   /* Don't use the JCL convert function because it throws an exception
+      on failure */
+@@ -288,9 +289,10 @@ Java_java_io_VMFile_isFile (JNIEnv * env,
+     }
+ 
+   result = cpio_checkType (filename, &entryType);
++  isfile = (result == CPNATIVE_OK && entryType == CPFILE_FILE ? 1 : 0);
+   (*env)->ReleaseStringUTFChars (env, name, filename);
+ 
+-  return result == CPNATIVE_OK && entryType == CPFILE_FILE ? 1 : 0;
++  return isfile;
+ #else /* not WITHOUT_FILESYSTEM */
+   return 0;
+ #endif /* not WITHOUT_FILESYSTEM */