This is a bit difficult to answer, as it depends on many factors.
In general, you can assume that you will get performance close to native apps for the GPU side, as the WebGLA JavaScript API that renders 2D and 3D graphics in a web browser. The Unity WebGL build option allows Unity to publish content as JavaScript programs which use HTML5 technologies and the WebGL rendering API to run Unity content in a web browser. More info
See in Glossary graphics API uses your GPU for hardware accelerated renderingThe process of drawing graphics to the screen (or to a render texture). By default, the main camera in Unity renders its view to the screen. More info
See in Glossary - there is just a little overhead for translating WebGL API calls and shadersA small script that contains the mathematical calculations and algorithms for calculating the Color of each pixel rendered, based on the lighting input and the Material configuration. More info
See in Glossary to your OS graphics API (typically DirectX on Windows or OpenGL on Mac or Linux).
For the CPU side, all your code is translated into asm.js JavaScript. So what kind of performance you can expect depends a lot on the JavaScript engine of the web browser used, and there are some pretty significant differences there currently. At the point of this writing (November 2015), Microsoft Edge and Mozilla Firefox deliver the best performance on Unity code, as these are currently the only browsers which make use of the asm.js spec to use an optimized AOT compilationAhead of Time (AOT) compilation is an iOS optimization method for optimizing the size of the built iOS player More info
See in Glossary path of JavaScript code for that case, which delivers performance within a factor of less then 2x slowdown compared to native code for many programming benchmarks - and that factor also matches results we’ve seen from different unity content we deployed to WebGL and ran in Firefox and Edge.
There are some other considerations, though. Currently, the JavaScript language does neither support multi-threading, nor SIMD. So, any code which benefits from these features will see bigger slowdowns then other code. You cannot write threading or SIMD code in WebGL in your scriptsA piece of code that allows you to create your own Components, trigger game events, modify Component properties over time and respond to user input in any way you like. More info
See in Glossary, but some engine parts are normally multi-threaded or SIMD optimized, and will run less performant on WebGL because of this. An example is the skinningThe process of binding bone joints to the vertices of a character’s mesh or ‘skin’. Performed with an external tool, such as Blender or Autodesk Maya. More info
See in Glossary code, which is both multi-threaded and SIMD-optimized. You can use the new timelineGeneric term within Unity that refers to all features, windows, editors, and components related to creating, modifying, or reusing cut-scenes, cinematics, and game-play sequences. More info
See in Glossary profilerA window that helps you to optimize your game. It shows how much time is spent in the various areas of your game. For example, it can report the percentage of time spent rendering, animating or in your game logic. More info
See in Glossary in Unity to see how Unity distributes work to different threads on non-WebGL platforms. Longer term, we are hoping that these features will become available on WebGL as well.
For best performance, set the optimization level to Fastest in the Build Player dialog, and set Exception support to None in the Player settings for WebGL.
The Unity profiler is supported in WebGL, see here how to set it up.
If Run in background is enabled in the Player settings for the WebGL platform, or if you enable Application.runInBackground, your content continues to run when the canvas or the browser window loses focus.
However, it should be noted that browsers may throttle content running in background tabs. If the tab with your content is not visible, your content will only be updated once a second in most browsers. Note that this will cause Time.time to progress slower than usual with the default settings, as the default value of Time.maximumDeltaTime is lower than one second.
You may want to run your WebGL content at a lower frame rate in some situations to reduce CPU usage. Like on other platforms, you can use the Application.targetFrameRate API to do so.
When you don’t want to throttle performance, set this API to the default value of –1, rather then to a high value. This allows the browser to adjust the frame rate for the smoothest animation in the browser’s render loop, and may produce better results than Unity trying to do its own main loop timing to match a target frame rate.