Kargil is governed under the unique administrative structure of the Union Territory of Ladakh. Local governance and development are managed by the Ladakh Autonomous Hill Development Council (LAHDC), Kargil. Established to give local people greater control over their region's development, the LAHDC consists of elected councilors representing various constituencies within the district, headed by a Chief Executive Councilor (CEC).
The executive head of the district is the Deputy Commissioner (DC) / District Magistrate, an officer of the Indian Administrative Service (IAS) who oversees law and order, land revenue, and the implementation of central government schemes.
Since Ladakh became a Union Territory without its own legislature in 2019, Kargil shares a single Member of Parliament (MP) in the Lok Sabha with Leh. The town is also the joint administrative capital of the UT, meaning various administrative departments rotate or operate in tandem between Leh and Kargil.