diff --git a/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/jar/NestedJarFile.java b/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/jar/NestedJarFile.java
index 2fe35c46c16..d711b9137a5 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/jar/NestedJarFile.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/jar/NestedJarFile.java
@@ -230,7 +230,7 @@ public class NestedJarFile extends JarFile {
 		}
 		ZipContent.Entry entry = getVersionedContentEntry(name);
 		if (entry != null) {
-			return false;
+			return true;
 		}
 		synchronized (this) {
 			ensureOpen();
diff --git a/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/net/protocol/jar/UrlJarFileFactory.java b/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/net/protocol/jar/UrlJarFileFactory.java
index 7a45caea98a..35ba9283ca9 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/net/protocol/jar/UrlJarFileFactory.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/net/protocol/jar/UrlJarFileFactory.java
@@ -58,7 +58,12 @@ class UrlJarFileFactory {
 	}
 
 	private Runtime.Version getVersion(URL url) {
-		return "runtime".equals(url.getRef()) ? JarFile.runtimeVersion() : JarFile.baseVersion();
+		// The standard JDK handler uses #runtime to indicate that the runtime version
+		// should be used. This unfortunately doesn't work for us as
+		// jdk.internal.loaderURLClassPath only adds the runtime fragment when the URL
+		// is using the internal JDK handler. We need to flip the default to use
+		// the runtime version. See gh-38050
+		return "base".equals(url.getRef()) ? JarFile.baseVersion() : JarFile.runtimeVersion();
 	}
 
 	private boolean isLocalFileUrl(URL url) {