The player controls a selected Yoshi from a side view. Each course requires Yoshi to reach the goal while carrying Baby Mario, who is separated from Yoshi when hit. A countdown timer gives Yoshi a chance to recover the baby before enemies capture him.

Yoshi can swallow enemies, create eggs, throw eggs at targets, flutter after jumping, ground-pound objects, and use special transformations. Courses contain flowers, red coins, stars, bonus areas, and hidden exits. Six worlds provide multiple stages, boss encounters, and optional challenge stages, with scores based on collected items and Baby Mario's protection.

Keep Baby Mario's star counter high by avoiding unnecessary hits; a full counter provides the most recovery time after an attack.

Explore before reaching the goal. Red coins can be disguised among ordinary coins, and flowers, bonus rooms, and hidden paths often require eggs, ground pounds, or transformations. Save eggs for switches and distant targets, and use flutter jumps to correct long airborne movements.