Patients considering or engaged in exercise as treatment may expect or experience transient increases in joint pain, causing fear of exercise and influencing compliance. This study investigated the pain trajectory during an 8-week neuromuscular exercise (NEMEX) program together with acute exercise-induced pain flares in persons with knee or hip pain.Individuals above 35 years self-reporting persistent knee or hip pain for the past 3 months were offered 8 weeks of supervised NEMEX, performed in groups twice weekly. The program consisted of 11 exercises focusing on joint stability and neuromuscular control. Participants self-reported joint pain on a 0-10 numerical rating scale (NRS) at baseline and 8-weeks follow-up. NRS pain ratings were also collected before and immediately after every attended exercise session.Joint pain was reduced from baseline (NRS 3.6; 95% CI 3.2-4.1) to 8-weeks follow-up (2.6; 95% CI 2.1-3.1), (P < 0.01). Pain decreased 0.04 NRS (95% CI 0.02-0.05, P < 0.01) on average per exercise session and pre- to post-exercise pain decreased 0.04 NRS (95% CI 0.03-0.05, P < 0.01) on average per session, approaching no acute exercise-induced pain in the last weeks.This study found a clear decrease in size of acute exercise-induced pain flares with increasing number of exercise sessions. In parallel, pain ratings decreased over the 8 weeks exercise period. Our findings provide helpful information for clinicians, which can be used to educate and balance patient expectation when starting supervised neuromuscular exercise.