You will encounter Jester's boss portal 3 times during the story. The very first time, fighting him is mandatory and is required to continue with the level. The other 2 times are miss-able, though you would have to be deliberately missing them as they are not the easiest things to avoid.
The portals are located on:
Mission Five: At the start of the mission and is impossible to miss.
Mission Twelve:, In the room with the spiral staircase that leads to the boss Geryon. This portal is miss-able.
Mission Seventeen: In the room that was the entrance to the three different trials earlier on in the story. This portal is miss-able.
Beating jester is fairly straightforward. On all 3 fights, just shoot at him with Ebony and Ivory untill he fans himself off with his staff, then get in there and beat him with your devil arm of choice. He will then teleport and put a sheild around himself, spawning balls that will damage you. Avoid them untill his sheild disapears, then you must shoot at him untill he fans off again. Repeat and rinse.
On the second and third fights, he will summon a ball shaped head, allowing him to take more damage and to attack you. However if you use the tactic above you'll be able to kill him except this time you will attack the ball, not the clown.