It is good to have the FXML format available as a useful notation for UIs. Unfortunately the design is unnecessary strongly married with the Java programming language and Java way of doing things. For users of other JVM languages, such as Clojure, it is consequently not usable in its current state (although it is advertised as: "You can use FXML with any Java Virtual Machine (JVM) language, such as Java, Scala, or Clojure.").

The problem lies in the coupling of UI components with event controllers. The static load method of the FXMLLoader expects that there is an existing Controller class. But in Clojure people don't create classes. They create functions, which will do the event handling. So I can not load an .fxml file, cause that runs into an exception, as it can't find the Controller class. There is none. Here a snippet of the ClassNotFoundException:

 0: URLClassLoader.java:366 java.net.URLClassLoader$1.run
 1: URLClassLoader.java:355 java.net.URLClassLoader$1.run
 2: (Unknown Source) java.security.AccessController.doPrivileged
 3: URLClassLoader.java:354 java.net.URLClassLoader.findClass
 4: ClassLoader.java:423 java.lang.ClassLoader.loadClass
 5: Launcher.java:308 sun.misc.Launcher$AppClassLoader.loadClass
 6: ClassLoader.java:356 java.lang.ClassLoader.loadClass
 7: FXMLLoader.java:726 javafx.fxml.FXMLLoader$ValueElement.processAttribute
 8: FXMLLoader.java:777 javafx.fxml.FXMLLoader$InstanceDeclarationElement.processAttribute
 9: FXMLLoader.java:182 javafx.fxml.FXMLLoader$Element.processStartElement
10: FXMLLoader.java:565 javafx.fxml.FXMLLoader$ValueElement.processStartElement
11: FXMLLoader.java:2305 javafx.fxml.FXMLLoader.processStartElement
12: FXMLLoader.java:2124 javafx.fxml.FXMLLoader.load
13: FXMLLoader.java:2021 javafx.fxml.FXMLLoader.load
14: FXMLLoader.java:2733 javafx.fxml.FXMLLoader.load
15: FXMLLoader.java:2712 javafx.fxml.FXMLLoader.load
16: FXMLLoader.java:2698 javafx.fxml.FXMLLoader.load
17: FXMLLoader.java:2685 javafx.fxml.FXMLLoader.load
18: FXMLLoader.java:2674 javafx.fxml.FXMLLoader.load


In a perfect world, I could just name the handler functions in the .fxml file, where the handlers are written in Clojure. For example, in http://docs.oracle.com/javafx/2/get_started/fxml_example.fxml.html I would not say fx:controller="fxmlexample.FXMLExampleController" but instead fx:controllerNS="my.clojure.namespace". And instead of onAction="#handleSubmitButtonAction" I would say onAction="handle-submit-button-action", which refers to a simple Clojure function:

(defn handle-submit-button-action [event]
  (.setText my-text-field "Sign in button pressed"))


I understand that in the current project phase you have no full-time Clojure developer, who could implement that, and always make sure that JFX is perfectly usable from Clojure too. But there might be a simple way how you could improve the FXML file format and its loader in a way, so that it can be used at least partially from Clojure.
And to do that one would have to specify in the .fxml file something like fx:noController="true". This flag would signal the loader to not try loading a controller class and ignore all onSomeEvent settings, such as onAction="#handleSubmitButtonAction". In the case of the linked fxml_example.fxml file above the loader would return and instance of the GridPane, with all its components, but without any event handling. On the Clojure side I would grab those components via their ID and attach the required handlers to them, in the Clojure code.