Choosing where to dig is a crucial element of the game's various puzzles, as creating holes in the wrong areas could hinder the player's efforts to advance.

[4] Readers of Family Computer Magazine voted to give the game a 22.1 out of 30 score in a 1998 public poll.

[10] Four writers of Nintendo Power drew comparison with HAL Laboratory's Eggerland series, citing the game's mix of action and puzzle elements.

They commended its catchy music, challenge, multiplayer, and Super Game Boy enhancements, but saw the uneven combination of simple and complex puzzles within a single level to be a negative point.

[8] Dave McComb of Nintendo Magazine System (Official Nintendo Magazine) praised the game's visuals for its simple but effective sprites, addictive gameplay, puzzles, boss battles, and two-player mode, but found the audio department to be average and noted the lack of additional replay value.

[3] Mega Fun's Ulf Schneider considered Mole Mania to be difficult puzzle game, noting that each level requires a very planned approach.

[6] IGN's Steve Averett gave the game positive remarks for its audiovisual presentation, non-linear format, and versus mode.

[13] Nintendo Life's Philip J. Reed commended the game for its crisp visuals, amusing cutscenes, and soundtrack.