Thiksey is administered as a village within the Leh district of the Union Territory of Ladakh. Local governance is handled by a Gram Panchayat (village council), headed by a Sarpanch, which manages day-to-day village affairs, minor disputes, and local development projects.
On a broader administrative level, Thiksey falls under the jurisdiction of the Ladakh Autonomous Hill Development Council (LAHDC), Leh. The LAHDC is a uniquely structured local government body that makes decisions regarding economic development, healthcare, education, and land use for the district. Thiksey is represented by a locally elected councilor in the LAHDC. Public services, including road maintenance, are heavily supported by the central government and the Border Roads Organization (BRO) due to the region's strategic importance.