Background: Emerging evidence suggests that aberrantly expressed microRNAs (miRNAs) participate in endometriosis pathogenesis. miR-1229-5p participates in the pathogenesis of several disease, but its precise role and mechanism in endometriosis is unclear. Methods: Endometrial tissues were obtained from patients with endometriosis and healthy controls. RT-qPCR and western blotting were employed to detect the expression levels of genes and proteins, respectively. Transcriptome sequencing and luciferase reporter assay were utilized to identify the target of miR-1229-5p. CCK-8, transwell assay, wound healing assay and flow cytometry assay were performed to evaluate the functional roles of miR-1229-5p. Finally, the clinical significance of miR-1229-5p was furtherly analyzed. Results: MiR-1229-5p was upregulated in ectopic endometrium of ovarian endometriosis patients (n = 60) compared to normal endometria of controls (n = 40), and its expression also served as an indicator for endometriosis severity. STMN1 was identified as the target of miR-1229-5p by luciferase experiments, and its expression was significantly downregulated in ectopic endometrium. Functionally, miR-1229-5p overexpression promoted migration, invasion, and inhibited apoptosis of ESCs and Ishikawa cells. Meanwhile, upregulation of miR-1229-5p also facilitated the protein expression of Bcl-2, MMP2, MMP9, N-cadherin, and ZEB1, and repressed the protein levels of Bax and E-cadherin. Whereas downregulation of miR-1229-5p exerted opposite effects. Importantly, STMN1 overexpression could partially reverse the effects of miR-1229-5p upregulation. Mechanistically, miR-1229-5p activates the p38 mitogen-activated protein kinase (p38 MAPK) signaling via targeting STMN1. Conclusion: The newly identified miR-1229-5p-STMN1-p38 MAPK axis illustrates the molecular mechanism of endometriosis progression and offers a potential therapeutic target for treating endometriosis.