This study analyzes the prevalence of health counseling related to physical activity among users of primary health care, and explores the associated variables. This cross-sectional study included a random sample of 4,060 adults and 4,003 older adults living in areas covered by primary health care in 41 cities from seven States of South and Northeast Brazil. Prevalence of counseling for physical activity was 28.9% (95%CI: 27.3-30.4) for adults and 38.9% (95%CI: 37.3-40.6) for elders. Prevalence was consistently higher among older adults, in the Northeast, and in areas covered by the Family Health Program. Gender, socioeconomic status, smoking, sedentary lifestyle, self-reported chronic non-communicable diseases, and continuous-use medication were also associated with the outcome. Counseling for physical activity at community health centers is under-promoted, considering individual needs for healthy living. There is a need to improve participation by health professionals from different fields to promote physical activity and other healthy behaviors.