The risk of chronic haemophilic arthropathy (CHA) is related to severity. Evidence suggests that primary prophylaxis (PPr) could reduce CHA incidence and its impact on quality of life. To evaluate the association between PPr and CHA in Colombian males with haemophilia B (HB) during 2015 to 2019. A panel-time analysis was performed with data provided by the National Health System to update a nationwide open cohort of people with congenital coagulopathies. The association was evaluated in a logistic random-effect regression model (LRERM), adjusted by age at diagnosis, prophylaxis dose and frequency, severity, haemarthrosis and high-titre inhibitors. During 2015-2019, a total of 362 men with HB and treated with either, primary, secondary or tertiary prophylaxis were identified. At baseline, CHA prevalence in the cohort was 36.84% (n=133), median age was 19.0years (IQR: 10.0-27.0), and median age at diagnosis was 1.0year (IQR: 0.0-4.0). PPr was prescribed in 37.85% (n=137), and median dose (IU/Kg/dose) was almost the same for primary vs. secondary/tertiary prophylaxis. Patients in PPr had a lower frequency of severe HB, CHA, haemarthrosis, infectious complications and high-titre inhibitors than those in secondary or tertiary prophylaxis (STPr). In the LRERM, PPr was associated with a significant reduction of 89.70% in the odds of CHA (aOR=0.103, IC 95%: 0.040, 0.270; P<.001), compared with STPr. PPr decreased the odds of CHA by 89.70% in males with HB in Colombia. Our findings are consistent with previous studies and support the strategy to prescribe PPr to our patients.