Solid-pseudopapillary neoplasm (SPN) of the pancreas is a low-grade malignant tumour, that mainly affects young females. Given its typical clinical characteristics, histopathological morphology and immunohistochemical nuclear expression of β-catenin, it is usually not difficult to diagnose SPN. However, nuclear expression of β-catenin is occasionally negative or false negative in SPN, leading to a missed diagnosis. In this study, we aimed to investigate the clinical significance of CTNNB1 mutation detection for diagnosing SPN and explore the difference in clinicopathological characteristics between female and male patients at different ages. We detected point mutations in exon 3 of CTNNB1 in 74.3% (133/179) of SPNs by Sanger sequencing. The main mutation sites were D32 (26%), S33 (23%), S37 (21%), G34 (14%) and T41 (11%). In the 3 SPNs without nuclear expression of β-catenin, Sanger sequencing showed the S33C mutation in exon 3 of CTNNB1 in two cases but not in one case in which next-generation sequencing detected the S37C mutation. Therefore, for atypical cases, testing for CTNNB1 mutations can help in the accurate diagnosis of SPN. The median age of the 179 patients was 31 years (6 ~ 64 years), and there were 32 male patients (17.9%) in this cohort. The tumour size, Ki-67 index, and the negative rates of β-catenin nuclear expression and syn expression in the paediatric group were higher than those in youth group and old group (P < 0.05 for all). There was no significant difference in age, tumour site; tumour size; expression of β-catenin, CD10, PR, Vimentin or Syn; Ki-67 index; or proportion of CTNNB1 mutations between male and female patients (P < 0.05 for all). Compared with middle-aged and elderly patients, paediatric with SPN may be more prone to recurrence, and their immunohistochemical phenotype is more complex, requiring additional care in the diagnosis and postoperative follow-up.