We have previously shown that children with pediatric systemic lupus erythematosus (pSLE) have high incidence of anti-phospholipid antibodies (APLA) and reports suggest that presence of APLA can modify disease expression. While the frequency of APLA has been studied previously in adults with SLE, there is paucity of literature in children especially with regard to long-term follow-up. In the earlier study, we analyzed 27 pSLE patients for the prevalence of APLA; in the present study, we further reviewed the APLA status and its relation with clinical outcome of this cohort of patients over a further 7 year follow-up period. Out of the initial cohort of 27 patients, follow-up APLA testing was available in 21 patients who were tested for APLA at least once during this time. Seven (33.3 %) of these 21 patients were never positive for any of the APLA; 1 (4.8 %) was persistently positive; and 13 (61.9 %) were positive for APLA intermittently or at least once. Overall, APLA positivity for IgG, IgM anticardiolipin antibodies (ACA) and lupus anticoagulant (LA) was comparable, with positivity seen in 10 (47.6 %), 9 (42.9 %) and 9 (42.9 %) cases, respectively. Anti-β2 GP1 antibodies were tested in 11 patients on follow-up, of which 3 (27.3 %) showed positivity. In all, 10 (47.6 %) patients showed positivity for more than 1 APLA. Two (9.5 %) patients showed varying degrees of positivity for LA, ACA, and anti-β2 GP1 antibodies at different times, thereby showing the importance of checking for all APLAs at each time of testing. Out of these 21 patients, 3 (14.3 %) patients had thrombosis, and all 3 patients were positive for APLA. There were 2 (9.5 %) fatalities-both of these had thrombosis and were positive for APLA. Our study shows that pSLE patients on treatment frequently test positive for APLA. Thrombosis was infrequent in this cohort. However, when present it was associated with APLA positivity and high fatality in our experience. On the other hand, presence or persistence of these antibodies was not always associated with thrombosis. Our study suggests that pSLE children should be tested routinely for APLA, as this would identify patients with an increased risk of thrombotic complications. However, the frequency of repeat testing for APLA in those who test negative initially needs to be determined on a case-to-case basis.