Objective To investigate the safety and efficacy of mapping and ablating paroxysmal atrial fibrillation (PAF) by using remote magnetic navigation system (MNS, Niobe Ⅲ, Stereotaxis) vs manual navigation. Methods Totally 103 consecutive patients diagnosed as PAF in our department from October 2014 to November 2016 were enrolled in our study. They were randomly divided into MNS group [(n=53,7 males and 26 females, at an age of (65±13) years] and manual navigation group [(n=50,3 males and 27 females, at an age of (62±15) years]. Procedure time, ablation time, X-ray exposure time, and recurrence in 3 months’ follow-up were collected and compared between the 2 groups. Results Pulmonary vein isolation was accomplished in 52 cases from the MNS group, and in 49 cases of the manual navigation group. The success rate was 98% in both group, without significant difference (P>0.05). Compared with the manual navigation group, the MNS group had significantly longer procedure and ablation times, but obviously shorter X-ray exposure time (P<0.05). There was no notable difference in the recurrent rate between the MNS (10 cases) and manual navigation groups (12 cases) in 3 months after surgery (19% vs 24%, P>0.05). Conclusion In comparison with manual navigation, Niobe Ⅲ remote magnetic navigation system is safe and effective in mapping and ablation of PAF, and it reduces the X-ray exposure time.