Background: A supportive school-based physical activity environment (PAE) is integral to children's physical activity behaviors, but less understood is its association with academic achievement. We aimed to assess the association between PAE and academic performance and whether a stronger relationship exists in lower-income schools (LIS) compared to middle-income schools (MIS). Methods: Schoolchildren (grades 3rd to 5th) were recruited from 17 Massachusetts public schools. Schools were classified based on geographic characteristics and free/reduced-price lunch (FRPL) eligibility (LIS = 7, Median FRPL = 86%; MIS = 10, Median FRPL = 20%). PAE was measured using a 10-item survey. Mixed-effects logistic regression models were used to examine associations between PAE and scoring Advanced/Proficient on standardized Math and English Language Arts (ELA) tests. Results: Demographic characteristics differed between LIS (N = 278, 5% non-Hispanic white) and MIS (N = 297, 73% non-Hispanic white). In LIS, PAE was associated with Math (odds ratio = 5.40, 95% CI = 2.52-11.54 p < 0.001), but not ELA test scores (p > 0.05). There was no relationship between PAE and MIS test scores (p > 0.05). Schooltime moderate-to-vigorous physical activity was not associated with test scores (p > 0.05). Conclusions: A beneficial relationship exists between a high-PAE and test scores among LIS children, suggesting that the PAE may be associated with a more supportive environment and may be more fundamentally important for lower-income students.