The cookie management system and methods of the present solution address issues with rewriting cookie headers by handling cookies in the content layer of HTTP instead of the HTTP transaction layer. The present solution maintains cookie information for a browser via an intermediary and installs the correct cookie parameters in the browser via the HTTP content layer. Instead of using the headers of the HTTP transaction layer which may cause issues due to rewriting, the present solution manages the cookies outside of this layer. This avoids the browser managing the cookies incorrectly. Set cookies headers served from a server in response to client HTTP requests are removed by the intermediary. Cookie information from the headers are stored in a cookie jar on the intermediary. The intermediary delivers instructions and scripts via the content layer of the HTTP response to set the cookie in the browser. The scripts detect browser changes to the cookie and communicates the changes to the intermediary to update the cookie jar. With the present solution, the domain and path names of a cookie are set correctly on the browser when delivering content via a reverse proxy.