Pediatric antiphospholipid syndrome (APS) is characterized by vascular thromboses and multisystem involvement associated with persistently positive antiphospholipid antibodies testing. There is limited literature regarding risk factors for development of thrombosis and long-term thrombotic outcomes in pediatric APS. The objective of our study was to review our institutional experience with pediatric APS and thrombosis outcomes. We conducted a 20-year retrospective review to study the clinical features, management, and long-term outcomes of patients between ages 6 months and 18 years diagnosed with APS. Seventeen patients (7 female; 10 male), with median age at first thrombosis being 15.3 years (range: 0.63–17.98 years) were included. The median follow-up period was 4.3 years (range: 0.8–16.9 years). Venous thrombosis was noted in 11 patients (64.7%) with arterial events occurring in six patients (35.3%). Nine (53%) patients were noted to have primary APS. Recurrent and/or progressive thrombotic events occurred in 10 patients (58.8%), which is higher than reported literature. The median time for recurrence/progression was 1.4 years (range: 0.37–11.85 years). At the time of recurrence/progression, only two (20%) patients were at therapeutic levels of anticoagulation. The high recurrence rate with majority of patients not being on therapeutic levels of anticoagulation at the time of the event along with 60% of recurrent events occurring at least 1 year from first vascular event suggests the possible need for long-term anticoagulation. However, larger pediatric studies are required to assess the need for long-term/indefinite anticoagulation.