He hailed from Lingzhi 令支 (modern Qian'an 遷安, Hebei) and was only a very small scribe in the commandery of Zhuojun 涿郡, where he studied the Confucian Classics with Lu Zhi 盧植. He was later promoted to commandery aide (zhangshi 長史) over regions inhabited by non-Chinese tribes that were in a tributary relation to the Han court (shuguo). When Zhang Chun 張純 allied with the leader of the tribal federation of the Wuhuan 烏桓, "Qiuliju" 丘力居, to stage a rebellion against the rule of the Han dynasty, Gongsun Zan was dispatched to fight against the rebels. For his victory he was promoted to *commandant [suppressing] the barbarians (luxiaowei 虜校尉). From then on, he was feared as an able military adversary by the Wuhuan.
During the Yellow Turban uprising 黃巾起義, Gongsun Zan displayed a ruthless way of warfare to put down the rebellion in eastern China. He was awarded the title of General of advancing martiality (fenwu jiangjun 奮武將軍, not in Hucker) and was given the title of Marquis of Ji 薊侯. In 193 Gongsun Zan killed the regional governor (mu 牧) of Youzhou 幽州， Liu Yu 劉虞, and gained control over the whole northeast of China.
Constant warfare against other warlords and rebellions caused by the precarious economic situation in the province of Youzhou caused him for a desparate fight in Yijing 易京 (modern Xiongxian 雄縣, Hebei). The warlord Yuan Shao 袁紹 finally besieged the city, assailed it and thus drove Gongsun Zan into sucide.