Visual scripting in Stencyl is based on the MIT Scratch project, which was designed to teach programming. Script elements fit together like puzzle pieces, ensuring that data and function types cannot be mismatched.

The visual scripting system is internally translated to Haxe. The resulting scripts can be viewed and edited, and there is also a "code block" object for including raw Haxe in visual scripts. This is great for learning to code, and also for advanced users who can further optimize the scripts if necessary.

Starter Stencyl is identical to paid-plan versions except that it only allows publication to Flash, with a mandatory Stencyl splash screen. Commercial development is allowed with Starter Stencyl.