With the Empty website template you get just that essentially just an empty project consisting of a .sln and .suo file. With the ASP.NET website template you'll get a basic skeleton consisting of a Default.aspx page along with an associated code-behind file, empty App_Data folder, default web.config file, a project .sln and .suo file.
Also check below link for more information:
ASP.Net-What-is-the-difference-between-a-Web-Site-and-a-Web-Application[
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