The name Baghlan is derived from Bagolango or "image-temple", inscribed on the temple of Surkh Kotal during the reign of the Kushan emperor Kanishka in the early 2nd century CE.

[4] In the 13th century CE, a permanent garrison of Mongol troops was quartered in the Kunduz-Baghlan area, and in 1253 fell under the jurisdiction of Sali Noyan Tatar, appointed by Möngke Khan.

[7] In the mid-20th century, as Afghanistan became the target of international development from both the Western and Soviet world, agricultural-industrial projects were initiated in Baghlan.

[14] Large portions of Baghlan and neighbouring Samangan Province were under the sway of the Soviet-aligned Naderi clan, the hereditary Ismaili Sayeds (spiritual leaders) of Kayan.

Under their jurisdiction, was largely quiet and societally functional throughout the 1980s, with hospitals, schools, and administrative services, funded by the communist central government.

Despite the Naderi's alliance with the Communists, they also maintained positive relations with the Mujahideen as well, permitting them to move through the area provided they refrained from attacks.

[17] The relocation aimed to enhance public access to administrative offices, leveraging Puli Khumri's strategic location along the Kabul-Mazar highway.

The cabinet of Dr. Najibullah, led by Sultan Ali Keshtmand, initially proposed this move through declaration number 492 on March 1, 1989.

[18] As the 2001 Afghan War commenced, Ismaili leader Sayed Mansoor Naderi attempted to retake Baghlan from the Taliban.

The Jamiat were able to seize the capital of Pul-i Khumri before Naderi, who despite his strong backing among the Afghan Ismailis and Shia Hazaras, was unable to rally enough supporters to control the province.

Naderi failed to retake the capital in 2001 and 2003, in the latter event he negotiated a power-sharing agreement with the dominant Andarabi militias and made the Ismaili bastion of the Kayan Valley his base.

[22] The Warlord of Kayan is a significant and popular documentary movie, filmed in 1989 by Jeff B. Harmon, featuring the political and social landscape of Baghlan during the civil wars.