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Background Mucosal healing (MH) has become a perspective treatment target in patients with Crohn’s disease (CD). Data about the impact of MH on long-term outcome in pediatric patients are still scarce. Methods 76 pediatric patients with CD were evaluated retrospectively (2000–2015) in a tertiary care center. Based on MH achievement, they were divided into two groups (MH, n = 17 and No MH, n = 59). The primary endpoint was to assess the association of MH and the need for CD-related hospitalizations or surgery in pediatric patients with CD. Results The number of hospitalized patients was 24% in the MH group and 42% in the No MH group, P = 0.26. The total number of CD-related hospitalizations was not significant between the MH group and the No MH group (5 vs. 41, P = 0.15). The time to the first hospitalization was 24 months in MH and 21 months in No MH, p > 0.99. 24% patients in the MH group and 39% patients in the No MH group underwent CD-related operation, P = 0.39. Time to the first operation was 43 months for MH and 19 months for the No MH group, P = 0.13. The follow-up period was 91 months in the MH group and 80 months in the No MH group, P = 0.74. The use of infliximab was positively associated with MH, P = 0.002. Conclusions MH was not associated with fewer CD-related hospitalizations or operations in pediatric patients with CD during seven years of follow-up.