Asparaginase (Asp) is one of the most important drugs for treating acute lymphoblastic leukemia (ALL). However, off‐protocol Asp administration (OPAA) or hypersensitivity may disturb its pharmacokinetic profile. In this retrospective study, we sought to determine whether OPAA and hypersensitivity to Escherichia coli asparaginase (E coli Asp) impaired extramedullary relapse prevention in a pediatric ALL cohort treated according to SCMC‐ALL‐2005 protocol from 2005 to 2014 at the Shanghai Children's Medical Center (SCMC). In total, 676 patients were enrolled in this study, including 369 with OPAA and 60 exhibiting hypersensitivity to E coli Asp. At the end of the most recent follow‐up, 58 patients had extramedullary relapse. The 5‐year cumulative extramedullary relapse incidence in patients with OPAA was 11.01%, whereas that in patients without OPAA was 5.28% (P = .0036). Moreover, the 5‐year cumulative extramedullary relapse incidence in patients that exhibited hypersensitivity to E coli Asp was 16.48%, whereas that in patients without hypersensitivity was 7.59% (P = .0195). Concerning the relapse site, OPAA not only increased central nervous system (CNS) relapse but testicular relapse as well. Based on Fine and Gray multivariate analysis, OPAA and hypersensitivity to Asp were independent risk factors for extramedullary relapse. In conclusion, to prevent extramedullary relapse of ALL, adequate duration to administrate Asp was more important than the total dosage, and more attention should be paid to Asp inadequate due to hypersensitivity.