The city was named for West Point graduate John Mullan, who was in charge of selecting a wagon route (commonly called the Mullan Road) between Fort Benton (Montana) and Fort Walla Walla (Washington).
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The Walla Walla tribe had raided a trading post at Fort Walla Walla, and their chief, Peopeomoxmox (also known as Yellow Bird), had reportedly vowed to kill Washington Territorial Governor Isaac Stevens.