The simplest route is to just use System properties. You can set either a global default:
(System/setProperty "hystrix.command.default.execution.isolation.thread.timeoutInMilliseconds" "200")
or a command specific value:
(System/setProperty "hystrix.command.my-command.execution.isolation.thread.timeoutInMilliseconds" "200")
You can perform this in your -main method. If you are running a real web-app sans -main, you can add a ring init in project.clj :ring {:handler your-handler :init your-config-method} your-config-method will be invoked on startup.