The outbreak of the Tajikistani Civil War complicated matters as most of Tajikistan's southern border region (Khatlon and Gorno-Badakhshan) was contested between Tajik government forces (and allied Russian border guards) and the United Tajik Opposition, which was supported by forces of the Islamic State of Afghanistan.

The Tajik opposition leaders enjoyed the support of the Afghan government and based themselves there, mainly Badakhshan Province.

[7] Presidents Emomalii Rahmon of Tajikistan and Hamid Karzai of Afghanistan meet on the sidelines of the 2004 Economic Cooperation Organization summit held in Dushanbe.

[9] Afghanistan and Tajikistan share a roughly 1,300-kilometer (810 mi) border, most of which is in rugged terrain and is poorly protected.

[10][11] Prior to the August 2021 takeover of Afghanistan by Taliban, transportation links between the two countries, such as the Afghanistan-Tajikistan Bridge, were slowly being rebuilt, often with help and financing from external governments.

A $500 million deal was signed in September 2007 to create an energy connection from Tajikistan and Kyrgyzstan to Afghanistan.

Both Tajikistan and Kyrgyzstan are trying to develop their potentially vast hydroelectric industry by selling it to South Asia, and an energy link with Afghanistan is seen as the first step in such expansion.