Despite a growing population of homeschool children in the United States, little is known regarding their physical activity (PA) levels. Without access to physical education, homeschool children may engage in inadequate PA levels. The purpose of this study was to objectively examine the activity levels of homeschool students participating in a Physical Education program. Seventy-two homeschool children (19 girls) participated in a once-weekly structured Physical Education program over a four-month period with a subsample of children participating in basketball. Pedometers/ accelerometers provided steps/session while accelerometers provided percentage of time in sedentary behavior (SB), light PA (LPA), and moderate-to-vigorous PA (MVPA). Children spent 69.7%, 18.9%, and 8.6% of their time in SB, LPA, and MVPA, respectively. A significant moderate correlation (r = 0.53, p < 0.01) between pedometer- and accelerometer-measured steps/session was found. Significant group differences among SB, LPA and MVPA, and steps/session were only present for steps/session (ß = 0.49, p = 0.02) with a marginally significant difference seen for MVPA (ß = 3.6, p = 0.07). No significant gender differences were seen on percentage of time in SB, LPA, or MVPA. Results indicated that participation in a Physical Education program may contribute to increasing PA levels of homeschool children. It is recommended that future programs focus on increasing time spent in MVPA.