How to popup an Alert on Button Click from code behind in Asp.net 2.0?
You can try this out.
string script = "alert(\"Hello!\");";
    ScriptManager.RegisterStartupScript(this,this.GetType(),
                  "ServerControlScript", script, true);
 or 
 ScriptManager.RegisterStartupScript(this.GetType() , 
"alerts", "javascript:alert('Hello')", ,true);