The current highway is the third to carry the M-99 designation. The others were located near Lake Michigan near Muskegon in the Lower Peninsula and Gulliver in the Upper Peninsula in the 1920s and 1930s. The current highway was first designated as parts of M-34 and M-64 in 1919. These numbers were later dropped in favor of an M-9 designation in 1929. For part of 1934, a loop route was designated M-158 in Hillsdale County that was used for a rerouted M-9 in the area. The M-99 designation was applied to the highway in 1940. Since then, the state has completed paving twice; one segment was returned to gravel surface for two years in the 1950s. The southern section in Hillsdale County was rerouted in the 1960s, and sections were converted into divided highways in the late 1970s.