Domestic flights go between Dushanbe and Khujand with Somon Air and Tajik Air. They both have online booking, but for regional flights the sites (they use the same system) doesn’t seem to work. The other domestic flight is the infamous Dushanbe – Khorog flight.
We recommend having a look at the flight map of Dushanbe and Khujand airport. Almaty, Bishkek and Tashkent are the major airports of the region. If you are planning to make a tour of the region, it makes sense to fly to any of these and then make your way overland to Tajikistan.