Abstract: Objective To evaluate the efficacy and safety of navigated endoscopic port surgery (EPS) for resection of intracerebral deep-seated small lesions. Methods From June 2010 to July 2015, 31 consecutive patients with intra-parenchymal deepseated (operative trajectory distance longer than 2 cm) and small lesions (diameter less than 2 cm) were enrolled in this study. Conventional frameless stereotactic guided micro-surgery was performed in 15 (48.4%) patients (control group), while in the other 16 (51.6%) patients, navigated EPS was performed (experiment group). 1.5T intra-operative MRI (iMRI) was used in all cases for the compensation of “brain shift” and updating navigation system. The iMRI scan times, duration of operation, and numbers of total resection of lesion were recorded and analyzed. All patients were followed up with both clinical examination and imaging methods. The short-term (＜ 3 months) and long-term (≥3 months) complication were also evaluated. Results There were no significant differences between two groups in mean age, gender ratio and the volume of lesions (P＞ 0.05). The mean iMRI scan times of control group was 1.67 times (total 25 times), and the average duration of procedure was 280 min with total resection of the lesions achieved in 14 cases. For the experiment group, the mean scan times was 1.19 times (total 19 times), and the average duration of procedure was 168 min with total resection of the lesions achieved in 15 cases. There were significant differences in the mean scan times and average duration of procedure between two groups (P＜ 0.05). However, no significant difference was found for the number of totally resected lesion (P＞ 0.05). There was no perioperative death and new technical-related complications. After a median follow-up of 33.5 months, no recurrence or lesion progression was found. Conclusion Navigated EPS provides high accuracy and efficacy for lesion targeting. Our preliminary results suggest that navigated EPS is a technically feasible and safe minimally invasive technique for intra-cerebral deep-seated small lesions.