Numerous municipalities in Michigan span two counties, but Fenton is one of two municipalities in the state of Michigan to span three counties; the other being the capital city of Lansing. The overwhelming majority of Fenton is located within Genesee County, with a total area of , of which is land and is water. The Genesee County portion represents 98.29% of Fenton's total area and 99.99% of its population. Of Fenton's 11,747 residents, all but 10 residents live in Genesee County. The separate 10 residents live in the Livingston County portion of Fenton, which contains a land area of . A minuscule portion with no residents extends into Oakland County with a total land area of .  