Growing pressure to develop public lands for renewable energy production places several protected species at increased risk of habitat loss. One example is the Mojave desert tortoise (Gopherus agassizii), a species often at the center of conflicts over public land development. For this species and others on public lands, a better understanding of their habitat needs can help minimize negative impacts and facilitate protection or restoration of habitat. We used radio-telemetry to track 46 neonate and juvenile tortoises in the Eastern Mojave Desert, California, USA, to quantify habitat at tortoise locations and paired random points to assess habitat selection. Tortoise locations near burrows were more likely to be under canopy cover and had greater coverage of perennial plants (especially creosote [Larrea tridentata]), more coverage by washes, a greater number of small-mammal burrows, and fewer white bursage (Ambrosia dumosa) than random points. Active tortoise locations away from burrows were closer to washes and perennial plants than were random points. Our results can help planners locate juvenile tortoises and avoid impacts to habitat critical for this life stage. Additionally, our results provide targets for habitat protection and restoration and suggest that diverse and abundant small-mammal populations and the availability of creosote bush are vital for juvenile desert tortoises in the Eastern Mojave Desert.