A native of Hyōgo prefecture, Fujiwara graduated from the 43rd class of the Imperial Japanese Army Academy in 1931 and was assigned to the IJA 37th Infantry Regiment.

In 1939, Fujiwara was transferred to the military intelligence unit within the Imperial Japanese Army General Staff, tasked with planning operations in south and Southeast Asia.

In 1941 Fujiwara established the F Kikan, a Japanese special operations unit, which was tasked with developing and assisting independence movements in British India, Malaya and Netherlands East Indies.

One of his first contacts was Sahid Abu Bakar, a religious teacher who lived in Kedah, who assisted him in recruiting a small organization to gather military intelligence, secure supplies, spread pro-Japanese propaganda, and to hinder Dutch efforts to sabotage local infrastructure.

In the Amazon Prime Video Original Series The Forgotten Army - Azaadi Ke Liye, Iwaichi Fujiwara is portrayed by a London-based Japanese actor Junichi Kajioka.