The default settings for JCE Editor will not allow you to add <script> tags, CSS settings (other than inline styling) or PHP within your content area. This is a safety feature for in the case of multiple people adding content or when you have comments enabled, you can't have some malicious programmer do unpleasant things to your site. It also allows for more control over how content is entered.

There may be cases where you want to be able to add the ability to include <script> tags, or other features, using JCE Editor. A good example is adding Google Ads or other ads, or if you need to have other tracking code or functionality that requires JavaScript or PHP. 

To allow JavaScript, PHP, CSS or XHTML you need to go into the JCE Editor Administration area.

Components -> JCE Editor -> Profiles

From the list, choose the appropriate User Profile for adding JavaScript into content. If you allow comments on your site, it is not recommended that you change the settings for the Front End profile. For this example, the site has only one contributor, so we will be changing the Default Profile.

From withing the Editor Profile section, choose the Editor Parameters tab. Then select Advanced on the left. 

The Advanced screen gives you several options for control over the content on your site. If you wish to allow Javascript, select the Yes radio button. Select Save & Close at the top. You can now add <script> tags to your content.

Note: When you go to add the <script> content for your individual Article or Module, you will need to click on Toggle Editor and add the <script>...</script> content in pure HTML mode. If you flip the editor back to the editor, you will see only a small icon  to indicate that there is JavaScript in this area.