Background: The US Centers for Disease Control and Prevention (CDC) promotes school-based strategies to increase physical activity (PA). Implementation feasibility and effect of these interventions on cardiovascular fitness (CVF) is unknown. Methods: Forty-nine low-SES schools were randomly assigned to either (1) continue routine PA programs (N = 24 schools, 2399 students) or (2) implement 4 CDC-based PA strategies (N = 25 schools, 2495 students). CVF assessed by PACER (Progressive Aerobic Cardiovascular Endurance Run) was obtained at the beginning and end of the school year. A post-study questionnaire was administered at each school to assess adherence. Results: Overall, PACER z-scores were not augmented by CDC-based PA strategies. In boys, PACER z-scores increased similarly in both intervention and control schools. In girls, increased mean PACER z-score was greater in control schools (p < 0.01). Fifty-two percent of intervention school's staff reported inability to implement or sustain 4 CDC-based PA strategies. Conclusions: Planned implementation of school-based CDC PA strategies did not increase CVF compared to routine PA programming. Lack of efficacy in girls suggests need for sex-specific targeted strategies. These findings highlight limited efficacy of CDC-based PA recommendations alone in low-SES schools. Schools may require additional support to successfully implement recommendations and meaningfully affect health outcomes.