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Objectives There is no consensus on canakinumab treatment tapering and discontinuation strategies in colchicine-resistant familial Mediterranean fever (FMF) patients. In this study, we aimed to establish a treatment management and discontinuation protocol in pediatric FMF patients treated with canakinumab. Methods Fifty-eight FMF patients treated with canakinumab were included. Since 2020, we have applied a protocol based on our experience that canakinumab is administered monthly at first six months, followed by bimonthly for six months, and a final period of every three months (for six months). The patients were divided into two groups as 2012–2019 (group A) and 2020–2022 (group B). Results In group A (n = 33), the median duration of canakinumab treatment was 2.5(1.9–3.7) years. Twenty-five out of 33 patients discontinued canakinumab after a median of 2.1 (1.8–3.4) years. In two patients, canakinumab was restarted because of relapse. In group B (n = 25), canakinumab was discontinued in 18 patients at the end of 18 months. After a median follow-up of 0.8 (0.6–1.1) years, two patients of them had a relapse and canakinumab treatment was re-initiated. The remaining 16 patients still have clinically inactive disease and are receiving only colchicine. When we compared the characteristics between groups A and B, there were no significant differences regarding demographic, clinical features, and outcomes. Conclusion This is the largest study in the literature suggesting a protocol for discontinuing canakinumab in pediatric FMF patients. It was possible to discontinue canakinumab successfully in more than half of the patients in 18 months. Thus, we suggest that this protocol can be used in pediatric FMF patients.