While SNES players got to play a 16-bit remake of NES Ms. Pac-Man in the two Game Centers, after they had collected all three video cartridges, Sega Genesis players got to play an all-new game named Pac-Jr.; it is not a conversion of Bally Midway's 1983 arcade game Jr. Pac-Man (as its title implies) but it is that game's opening theme you will hear from the Yamaha YM-2612 at the start. It is also the first game from Namco to display its year next to a copyright symbol and the company's logo since New Rally-X back in 1981 - and its four mazes are based on those of the aforementioned Ms. Pac-Man, but with a few alterations. The first maze contains 166 pellets (170 if you count the power pellets), the second one contains 204 pellets (208 if you count the power pellets), the third one contains 201 pellets (205 if you count the power pellets, which is the first odd-numbered pellet total in a Pac-Man game) and the fourth one contains 192 pellets (196 if you count the power pellets); but much like in Ms. Pac-Man, the game will alternate between the third and fourth mazes every four rounds after the thirteenth round, and their colouring will have been changed to pink and orange (not lilac and pink) respectively.
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Maze 1 (Rounds 1-2)
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Maze 2 (Rounds 3-5)
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Maze 3 (Rounds 6-9)
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Maze 4 (Rounds 10-13)
Seven new bonus items have also been introduced; much like in Ms. Pac-Man, they will enter the mazes through the warp tunnels, then bounce around them before eventually leaving. After the seventh round, the items which appear are still randomly-generated - but they will all still be worth 5000 points.
| Round | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
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| Points | 100 | 200 | 500 | 700 | 1000 | 2000 | 5000 |
Pac-Man himself has also eaten sneakers for that seventh round of Super Pac-Man back in 1982, and there are also three new "episodic" intermissions:
- Scene 1: Run For Your Life: Pac-Jr. is chased off the left side of the screen by Blinky, then back off the right side of the screen by Blinky and Pinky, then back off the left side of the screen by Blinky, Pinky and Inky, then back off the right side of the screen by Blinky, Pinky, Inky, and Clyde (not Tim from the original Jr. Pac-Man); this intermission will be shown after clearing the second round, and is the equivalent of They Meet from Ms. Pac-Man.
- Scene 2: Strike Them Out: Pac-Jr. is chased off the left side of the screen by all four ghosts, but when they almost chase him back off the right side of the screen again, he stops, turns around and throws a World Stadium-style baseball at them which lands on each of them in turn; this intermission will be shown after clearing the fifth round and is the equivalent of The Chase in Ms. Pac-Man. There is just one more all-new intermission to go now.
- Scene 3: The Reunion: Pac-Jr. stands in the centre of the screen, as both his father and mother run into view (from its left and right sides), and they all then run off the right side of the screen together; this intermission will be shown after clearing the ninth, thirteenth, and seventeenth rounds, and is the equivalent of Junior in Ms. Pac-Man. It is also worth noting that for the SNES remake of the Junior cutscene, the stork was graphically enhanced.