I was having an issue more complex because I have more than one file with same name, one is in the main Spring Boot jar and others are in jars inside main fat jar. My solution was getting all the resources with same name and after that get the one I needed filtering by package name. To get all the files:
ResourceLoader resourceLoader = new FileSystemResourceLoader();
final Enumeration<URL> systemResources = resourceLoader.getClassLoader().getResources(fileNameWithoutExt + FILE_EXT);