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S.T.A.L.K.E.R.: Clear Sky, is the prequel to S.T.A.L.K.E.R.: Shadow of Chernobyl, a first-person shooter survival horror video game with RPG elements by Ukrainian developer GSC Game World. The game consists of a roughly 50/50 mix of new areas and old, remodeled areas from the previous game. The X-ray graphics engine has been updated to version 1.5 and includes DirectX 10 support (later patch 1.5.06 included DirectX 10.1). Additionally, the AI received an overhaul to accommodate the new faction wars feature.

This game combines elements of first-person shooters ("twitch-based" aiming, with a first person perspective), survival horror (ammo scavenging, frightening atmosphere with powerful monsters), and RPGs (inventory management, quests, character interaction, armors and defense stats).

The most significant gameplay addition since Shadow of Chernobyl is the faction wars system. Different factions will struggle for territory, attacking to gain territory and then defending to keep it, while others then try to retake it. The player will be able to join and help factions in their battles. The stronger a faction becomes, the better equipment the traders can provide and their soldiers can use. The player character is a mercenary, and may do missions for any faction or remain completely neutral without disrupting the necessary progression of the game. Each of the main factions provide services, most importantly access to a trader and an engineer.

While Scar is always aligned with Clear Sky, and his ultimate goal is to defeat Strelok, he can fight against or ally with the four other factions in the Zone (Loners, Duty, Freedom and Bandits). The Swamp-dwelling Renegade or the Military factions cannot be joined. Careful choice of faction alignment needs to be considered in some parts of the story, for it may be difficult to progress further if the Stalker the player is interacting with is hostile, has needed information or is essential to triggering the next stage.

Other gameplay advancements since the first game include a deepened weapon customization system with the ability to repair damaged gear. Anomalies are harder to notice and now contain the artifacts in the game, which require a detector to locate. NPCs are given the ability to use hand grenades, take cover dynamically and use "blind-fire" techniques. Light machine guns have been introduced. There are NPC guides in the zone that will provide fast-travel for a fee. Emissions, powerful waves that are sometimes visible or invisible determinant on the intensity, unleash lethal radiation, psi-emissions and other unknown particles and energy directly from the Chernobyl Nuclear Power Plant, directly affecting the Noosphere in The Exclusion Zone, making it deadly to all lifeforms except specific mutants. Emissions also occur on an infrequent basis, requiring the player to take cover in a building pointed out by the PDA. If not adequately concealed, the player's nervous system shuts down, resulting in the player's death.