The objective of each stage of the game is to reach the end by shooting at every enemy that gets in the way, and fight the boss awaiting at the end. While most of the game have the character walking on foot, certain stages have the player riding a Motoroid, a hoverbike that can transform into an ostrich-like robot. Unlike previous Contra games, which featured overhead segments in addition to the regular side-view stages, all the stages in Hard Corps retains the standard side-view perspective for most of the game. Another difference is the player can now choose between one of four unique player characters. Like in the previous Contra games, a maximum of two players can play simultaneously, but they're not allowed to choose the same character.

The controls are similar to Contra III, but have been adapted to work with the Genesis's standard three-button controller, as well as the six-button controller. The three main buttons (A, B, and C) are used for switching between weapons, shooting, and jumping respectively in the default control configuration. By pressing the weapon change button while shooting (or the X, Y, or Z buttons on the six-button controller), the player can toggle between two shooting styles: one which allows for free movement while shooting, and another which keeps the character still while he or she aims in one of eight directions. The player can also jump down from certain platforms, as well as move on walls and ceilings like in Contra III. A new ability added to the game is a sliding technique performed by holding the direction-pad diagonally downwards while pressing the jump button. The character will be invulnerable while sliding and can even harm certain enemies.

The player can now carry up to four different weapons, as well as a supply of bombs. Like in previous games, weapons are obtained from flying capsule pods. This time the weapon items are now labeled "A", "B", "C", and "D", which will vary depending on the character controlled by the player. Each player begins with a standard machine gun, which can be upgraded to a different semi-automatic weapon by picking up the A-type power-up. When the player's character loses a life, the weapon they had equipped will be lost. Unlike Contra III, the player's supply of bombs will remain the same when a life is lost.

Another unique feature to Contra: Hard Corps is the addition of branching paths that allows the player to play through a different set of stages depending on key decisions made during key moments of the game's story.