If you want to register it inside an update panel use:
ScriptManager.RegisterClientScriptBlock(this, this.GetType(), "yourScriptName", "yourJavaScriptFunctionName()",true);
If you want to register the script on page load or without update panel use:
Page.ClientScript.RegisterStartupScript(this.GetType(), "yourScriptName", "yourJavaScriptFunctionName()",true);