Background: Abnormal respiration during radiofrequency catheter ablation (RFCA) with deep sedation in patients with atrial fibrillation (AF) can affect the procedure’s success. However, the respiratory pattern during RFCA with deep sedation remains unclear. This study aimed to investigate abnormal respiration during RFCA and its relationship with sleep apnea in patients with AF. Methods: We included patients with AF who underwent RFCA with cardiorespiratory monitoring using a portable polygraph both at night and during RFCA with deep sedation. The patients were divided based on the administered sedative medicines. Results: We included 40 patients with AF. An overnight sleep study revealed that 27 patients had sleep apnea; among them, 9 showed central predominance. During RFCA with deep sedation, 15 patients showed an abnormal respiratory pattern, with 14 patients showing obstructive predominance. Further, 17 and 23 patients were administered with propofol alone and dexmedetomidine plus propofol, respectively. There was no significant between-group difference in the respiratory event index (REI) at night (7.9 vs. 9.3, p = 0.744). However, compared with the group that received dexmedetomidine plus propofol, the propofol-alone group showed a higher REI during RFCA (5.4 vs. 2.6, p = 0.048), more frequent use of the airway (47% vs. 13%, p = 0.030), and a higher dose of administered propofol (3.9 mg/h/kg vs. 1.2 mg/h/kg, p 0.001). Multivariable analysis revealed that only the propofol amount was associated with REI during RFCA (p = 0.007). Conclusions: Our findings demonstrated that respiratory events during RFCA with deep sedation were mainly obstructive. Propofol should be administered with dexmedetomidine rather than alone to reduce the propofol amount and avoid respiratory instability.