If you want to execute JavaScript in code behind for example after an event, you can: ScriptManager.RegisterStartupScript(this, GetType(), "anyName", "myScript();", true);
When I directly put the following script in the markup of Master File. There is also some JavaScript error. It is because .aspx in different folder may using this master page, so javascript path may become incorrect. To solve it, you need to register the javascript in page_load method. Page.ClientScript.RegisterClientScriptInclude("jquery", ResolveUrl("~/Script/jquery-1.4.2.min.js"));