The family environment is associated with religiosity and spirituality as well as many aspects of adolescent lives, including their health behaviour. Therefore, the aim of this study was to assess family environment associations with adolescent religious attendance (RA), i.e., weekly participation in religious services, and spirituality in a highly secular country. A nationally representative sample (n = 4182, 14.4 ± 1.1 years, 48.6% boys) of Czech adolescents participated in the 2014 Health Behaviour in School-aged Children cross-sectional study. RA, spirituality and the family environment, i.e., family communication, perceived emotional support, and parental monitoring, were measured. Higher adolescent RA was associated with lower self-reported easiness of communication with mother (odds ratio (OR) = 0.68; 99% confidence interval (99% CI) = 0.47–0.99; p < 0.01). In contrast, spiritual respondents were more likely to report both easier communication with their father (OR per standard deviation (SD) change = 1.12, 99% CI 1.02–1.23; p < 0.01) and mother (OR per SD change = 1.38 (1.23–1.55); p < 0.001) and higher perceived emotional support (OR per SD change = 1.73 (1.55–1.92); p < 0.001). Parents of respondents who attended religious services at least once a week, as well as parents of spiritual respondents, were generally more likely to monitor adolescent behaviour. Thus, this study provides information for parents, mental health workers, and pastoral carers. Further research should assess the association of a lower easiness of family communication with dissonances in adolescent–parent religiosity/spirituality and with higher parental monitoring.