The pass was named after Lieutenant John Mullan, the army engineer who first crossed the pass on March 22, 1854, and later supervised construction of the Mullan Road, the first road over the pass, in 1860.
The name would not stick though and in 1865 Captain John Mullan, a U.S. Army Captain who was traveling through the area under orders to build the "Mullan Trail" from Walla Walla, Washington to Fort Benton, Montana after the discovery of silver in the central Idaho mountains along what today is the route of Interstate 90, would rename the lake Kaniksu.
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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).