If the script is inside in a separate file and pointed out through the source attribute, it is not loaded.

<fx:script source="myapp.js" />

When defining an FXML interface with <fx:script>, it only works when the script is bundled inside the tag.

<fx:script>
    var System = Packages.java.lang.System;

    function handleButtonAction(event) {
       System.out.println('You clicked me!');
    }
</fx:script>