A Crack in Time is a third person three dimensional action game with elements of platforming, shooting, role playing, puzzle solving and open exploration. The player controls Ratchet, a lombax who wields an arsenal of weapons, gadgets, and flies a sentient starship known as the Aphelion, and Clank, a robot trainee for the role of Caretaker in the Great Clock who can make use of his Chronoscepter to manipulate time. Ratchet retains much of his core moveset, as well as make use of the OmniWrench Millennium 12 ability to manipulate objects, with the main new addition being the hoverboots that allow him to traverse environments very quickly. Clank's use of the Chronoscepter and ability to create temporal recordings make his puzzle-solving gameplay vastly different from previous titles.
Gameplay is split between the duo, with Ratchet exploring the open segments of the Breegus System using the Aphelion, which can land on planets and moons to complete main and side objectives, which normally involve either platforming through linear sections or combat sections shooting enemies. Between planets and moons, Ratchet will fly the Aphelion in space combat, speak to new individuals to be set different objectives, and can also compete in the Agorian Battleplex arena to defeat waves of enemies. Main objectives completed continue the story, while side objectives award prizes in the form of bolts (currency used to purchase new weapons and armor), Zoni (used to upgrade the Aphelion), constructo mods (used to modify functionality of constructo weapons), gold bolts (used to unlock extras such as skins), or holo-plans for the RYNO V (which will grant Ratchet the weapon once all are collected).

Control will often switch to Clank, who is undergoing training to become the Senior Caretaker of the Great Clock. Clank must complete puzzle-solving objectives using temporal recordings to unlock paths forward, and also use the Chronoscepter in planet rooms to stop temporal anomalies on a planet. These are required both for main objectives to proceed with the story, and side objectives to unlock areas both for Ratchet and Clank to find hidden items.

After completing the game, the player can choose either to warp back before defeating the final boss, or proceed to replay the game in challenge mode, which allows Ratchet to keep all weapons with their respective upgrades and all Aphelion upgrades, and fight more powerful enemies. In this mode, Ratchet can purchase the Omega version of his weapons to upgrade them beyond the maximum. As these weapons are much more expensive, challenge mode has a bolt multiplier for enemies that were destroyed before Ratchet takes a hit.

New to the game, players can record their in-game statistics and showcase their preferred and customized constructo weapon using PlayStation Network.