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Background: Children from low-income families experience accelerated BMI gain and learning loss during summer. Healthy Summer Learners (HSL) addresses accelerated BMI gain and academic learning loss during summer by providing academic- and health-focused programming. This manuscript reports the effects of HSL on underlying obesogenic behaviors (i.e., physical activity, screen time, sleep, diet) that lead to accelerated summer BMI gain, a necessary first step to informing a future randomized controlled trial of HSL. Methods: In the summer of 2018 and 2019 using a quasi-experimental study design, 180 children (90 per summer, 7.9 years [SD = 1.0], 94% non-Hispanic Black, 40% male) at two schools (i.e., one per summer) who were struggling academically (25–75% on a standardized reading test) were provided a free, school-based 6-week health- and academic-focused summer program (i.e., HSL, n = 60), a 4- to 6-week academic-focused summer program (i.e., 21st Century Summer Learning program (21C), n = 60), or no summer program (n = 60). Children wore the Fitbit Charge 2™ over a 10-week period during the summers (June–Aug) of 2018–2019. Differences within (within child days attend vs. not attend) and between (differences between groups attend vs. not attend) were evaluated using mixed effects linear regression. Results: Regression estimates indicated that, on days attending, HSL children experienced a greater reduction in sedentary minutes (− 58.6 [95% CI = − 92.7, − 24.4]) and a greater increase in moderate-to-vigorous physical activity (MVPA) (36.2 [95% CI = 25.1, 47.3]) and steps (2799.2 [95% CI = 2114.2, 3484.2]) compared to 21C children. However, both HSL and 21C children were more active (i.e., greater MVPA, total steps) and less sedentary (i.e., less sedentary minutes and total screen time) and displayed better sleeping patterns (i.e., earlier and less variability in sleep onset and offset) on days they attended than children in the control. Conclusions: HSL produced greater changes in physical activity than 21C. However, attendance at either HSL or 21C leads to more healthy obesogenic behaviors. Based on the behavioral data in this pilot study, a larger trial may be warranted. These results must be considered along with the pending primary outcomes (i.e., academics and BMI z-score) of the HSL pilot to determine if a full-scale trial is warranted. Trial registration: NIH-NCT03321071. Registered 25 October 2017 [ABSTRACT FROM AUTHOR]