Background This study examined the joint associations of leisure time physical activity and television (TV) viewing time with the prevalence of chronic diseases among Brazilian adults. Methods Data from the Brazilian Health Survey, a nationally representative survey conducted in 2013 (n = 60 202; ≥18 years), were used. Time spent in TV viewing and leisure physical activity, physician diagnoses of diabetes, hypertension and heart disease and information on co-variables (chronological age, education, ethnicity, candies/sweets consumption, sodium intake and tobacco smoking) were collected via interview. Descriptive statistics (mean and 95% confidence interval) and logistic regression models were used for etiological analyses. Results Physical activity attenuated but did not eliminate the risk associated with high TV viewing for at least one chronic disease in the general population [odds ratio [OR]: 1.29 (1.11–1.50)] and among women [OR: 1.31 (1.09–1.60)], adults [OR: 1.24 (1.05–1.46)] and older adults [OR: 1.63 (1.05–2.53)]. On the other hand, physical activity eliminated the risk associated with high TV viewing for at least one chronic disease among men [OR: 1.24 (0.98–1.58)]. Conclusions We conclude that physical activity can attenuate but not eliminate the negative effects of high TV viewing on chronic disease among subgroups of Brazilian adults.