Background: Disparities in school attendance exist for children with medical complexity (CMC) due to COVID-19. Longitudinal changes in family-reported school safety perceptions and predictors of full-time, in-person school attendance are unknown. Methods: This was a prospective, longitudinal cohort study with 3 survey waves (June 2021-June 2022) among English- and Spanish-speaking families of CMC aged 5 to 17 years and pre-pandemic school attendance. Changes in Health Belief Model perceptions and full-time in-person school attendance were estimated using multivariate generalized linear modeling with repeated measures. Results: Among 1601 respondents (52.9% of 3073 invited), 86.8% participated in all 3 surveys. School safety perceptions improved with time; however, perceived susceptibility to COVID-19 increased. Full-time in-person school attendance rose from 48.4% to 90.0% from wave 1 to 3 (p < 0.0001), and was associated with motivation, benefits, and cues. For example, families with low compared to high motivation for in-person attendance had 76% versus 98% predicted probability for child's school attendance, respectively at wave 3 (p < 0.0001). Implications for School Health Policy, Practice, and Equity: Probability of full-time in-person school attendance was associated with several health belief model perceptions. School health policy and programs may benefit from promoting family motivation, benefits, and cues during future respiratory illness epidemics including COVID-19. Conclusions: In-person school attendance improved for CMC over time. Opportunities exist to continue optimizing in-person attendance and family-perceived safety for CMC at school.