Objective To investigate the clinical value of the application of electromagnetic neuronavigation in neuroendoscopic endonasal transsphenoidal pituitary tumor resection. Methods Forty patients with pituitary tumors admitted to the neurosurgery department of the First People's Hospital of Nanning from July 2020 to December 2022 were selected as the research subjects. The patients were divided into an observation group and a control group by random number method, with 20 cases in each group. The observation group underwent neuroendoscopic endonasal transsphenoidal pituitary tumor resection guided by electromagnetic neuronavigation, whereas the control group received conventional neuroendoscopic endonasal transsphenoidal pituitary tumor resection. Compare the surgical related indicators, surgical outcomes, complications, the pre- and post- surgical changes in hormone levels such as prolactin (PRL), growth hormone (GH), adrenocorticotropic hormone (ACTH), thyroid stimulating hormone (TSH), follicle stimulating hormone (FSH) between two groups of patients. Results There was no statistically significant difference in operation time, intraoperative blood loss, and postoperative hospitalization time between the two groups of patients (all P>0.05). The total removal rate of pituitary tumors in the observation group was higher than that in the control group, with statistically significant difference (P<0.05). Before surgery, as well as on the 1st, 3rd, and 7th days after surgery, there was no statistically significant difference in the levels of PRL, ACTH, and TSH between the two groups (all P>0.05). On the 1st, 3rd, and 7th days after surgery, the levels of GH and FSH in the obserbation group were significantly higher than those in the control group, with statistically significant differences (all P<0.05). The incidence of postoperative complications in the observation group was 30.00% (6/20), wheras that in the control group was 40.00% (8/20), with no statistically significant difference (P>0.05). Conclusion The application of electromagnetic neuronavigation in neuroendoscopic endonasal trans-sphenoidal pituitary tumor resection is safe and effective, which can obtain a higher tumor resection rate, and it is easy to use with accurate positioning.