Objective In this retrospective cohort study, we aim to investigate the most used biological disease modifying anti-rheumatic drugs (bDMARDs) in Juvenile Idiopathic Arthritis (JIA) patients in a pediatric rheumatologic unit from a Portuguese tertiary hospital, along with their effectiveness and safety. We also intended to link their effectiveness and the pathophysiology of the disease. Methods The medical records of JIA patients exposed to bDMARDs, between January 2018 and January 2023, in a pediatric rheumatologic unit from a Portuguese tertiary hospital were reviewed. Therapy effectiveness was accessed based on achievement of inactive disease according to Wallace Criteria. Effectiveness of different bDMARDs in the several JIA subtypes was linked to the disease´s pathophysiology. Adverse effects were also reviewed. Results Thirty-four patients were included in the study. Overall, nineteen patients (67,9%) had inactive disease at last evaluation. Six patients with missing data on inactive disease status were excluded from this analysis. Number of affected joints, ESR and CRP were significantly lower at 3, 6, 12 and 24 months after bDMARD therapy. All systemic JIA patients (n=10) were initially treated with Anakinra. Six (60%) achieved inactive disease. Two (20%) switched to Tocilizumab due to ineffectiveness in the control of articular features. Patients who switched to tocilizumab achieved inactive disease until the end of the follow-up. All patients with the other subtypes of JIA (n=24) were treated with TNF inhibitors. Inactive disease was achieved in 55,6%. Adverse effects occurred in eight patients (23,5%). Conclusions The results of the present study demonstrate the effectiveness of bDMARs in the study population. bDMARDs reduced the number of affected joints, CRP and ESR after three months of treatment, and this effectiveness was sustained over the two years of follow-up. For systemic JIA, preferred drug was Anakinra, an interleukin 1 inhibitor, and its effectiveness was consistent with previous studies. In the other JIA subtypes, TNF inhibitors were the most used bDMARDs, and showed an effectiveness consistent with previous studies. The most used bDMARDs for each JIA subtype are in line with pathophysiological differences. Our results demonstrated the safety of these drugs.