Here's a good video on the subject.  Note you could also just mortise both sides and cut some floating tenons, too.   Or you could go to PopWood's site and pay $4 for the video.

 

http://mycrafts.com/diy/mortise-tenon-joinery-with-a-router/

Thanks!

Have done it with router but used a router table. It is a bit tedious but when cutting 24 after setup is fast.

Before I had a CNC where I could clamp parts vertically I preferred to cut mortises on the router table just as Gerald mentioned. Tenons to fit I usually used the table saw to cut the shoulders then with a tenoning jig cut the sides.  Band saw to cut the ends and a chisel to nip the corners to fit in the round end mortise. While most of the glue is between the faces as the video stated a snug end help keep the joint from racking.  Getting the joint lined up was never a problem with careful layout.

4D