It was founded in the end of the 19th century as a sawmill serving the railway stop #39 (also known as Vaykulichi). Several Buryat uluses were located in the vicinity.
Mukhor-Shibirka was home to the administrations of three kolkhozes (Udarnik, imeni N. S. Khrushchyova, and Druzhba) during the 1930s–1960s, and its population was mostly employed in agriculture and railroad industry.