Lifestyle behaviors need to be more explored within the context of chronic noncommunicable disease (NCD) multimorbidity. This study aimed to investigate the association of multimorbidity with physical activity and sedentary behavior in a representative Brazilian population (n = 52,929). A cross-sectional survey (VIGITEL in the Portuguese acronym) was conducted in 2013 in the 27 Brazilian federal units. Multimorbidity is defined as the presence of two or more NCDs, that is, the outcome variable; and physical activity (commuting, domestic chores, leisure, and work domains) and sedentary behavior (television time < 2 hours/day and ≥ 2 hours/day) were the exposure variables. Poisson and multinomial logistic regressions (odds ratio - OR) stratified by age and their respective 95% confidence intervals were used, adopting a significance level of 5%. Among 37,947 adults, the presence of three chronic diseases was less frequent in subjects active in the work domain (OR = 0.60) and more frequent among those with longer daily television time (OR = 1.25). The presence of four diseases was less frequent in subjects active in the commuting (OR = 0.52) and work (OR = 0.42) domains. Among 14,982 older adults, the presence of two, three, and four chronic diseases was consistently more frequent in those with longer daily television time (OR = 1.33; 1.55 and 1.93, respectively). Finally, interactions between total physical activity level and daily television time were statistically significant in the multimorbidity in both age groups. Physical activity and sedentary behavior are associated with multimorbidity and should be considered independent factors for health promotion and for the treatment of patients with multimorbidity.