In order to travel to the Pamir Mountains, the Pamir Highway and the Gorno-Badakhshan Autonomous Region (GBAO), you will need a GBAO Permit. Since part of the Pamir Highway runs along the border with Afghanistan, this security measure is necessary and requires these additional papers. If you are applying for Tajikistan e-visa, you need to tick the corresponding box to apply for GBAO too and it will be issued with your visa.
The GBAO Permit will be checked at certain checkpoints along the Pamir Highway. You should make 10 copies of the permit in advance, as each checkpoint along the Pamir Highway will keep a copy. Permits can be obtained at Tajikistan embassies when applying for a visa, or at the OVIR (Department of Visas and Registration) Office in Dushanbe. All that is required is a passport.
When in Tajikistan, it takes 5-7 days to receive a GBAO Permit valid for the length of your visa that allows travel through the entire Gorno-Badakhshan Autonomous Region, except Sarez Lake and Zorkul. The price for getting a GBAO Permit through various travel agencies varies from 30 to 50 USD. GBAO Permits can be extended at any OVIR department along your route for a maximum of 30 days.
Permits for Sarez Lake can be obtained from the Committee of Emergency Situations and Civil Defense. According to official rules, the permit is free, but in practice it is issued rather rarely. Permits for Zorkul are issued at the Direction of State Reserves in Dushanbe. It usually costs 4 USD per day to stay at the Zorkul State Nature Reserve.