Migratory mule deer (Odocoileus hemionus) within the San Joaquin Watershed occupy most of the watershed above Kerckhoff Reservoir, Fresno and Madera Counties, California. Human infrastructure in the watershed is widespread and includes residential, water control, hydroelectric power, and recreational use developments. Steep topography between winter and summer range limit crossing points along the San Joaquin River. Habitat conditions favoring deer declined from a peak around 1950, resulting in a reduction in the deer population. The current deer population is believed to be about 4,000. A massive wildfire burned through most of the watershed in 2020, dramatically changing habitat conditions in some areas. These data provide the location of migration stopovers for mule deer in the Upper San Joaquin Watershed population in California. They were developed from 55 migration sequences collected from a sample size of 30 animals comprising GPS locations collected every 2-12 hours.