Limited comparative data are available regarding catheter ablation (CA) of atrial fibrillation (AF) using second-generation cryoballoon (CB-2) vs. radiofrequency (RF) ablation in elderly patients (> 75 years old). The present study aimed to compare the costs and clinical outcomes in elderly patients using these two strategies. Elderly patients with symptomatic drug-refractory paroxysmal/short-lasting persistent AF were included in the study. Pulmonary vein isolation (PVI) was performed in all patients. A total of 324 elderly patients were included (RF,176; CB-2,148) from September 2016 to April 2019. The CB-2 was associated with shorter procedure time and left atrial dwell time (112.9 ± 11.1 vs. 135.1 ± 9.9 min, P < 0.001; 53.7 ± 8.9 vs. 65.1.9 ± 9.0 min, P < 0.001) but marked fluoroscopy utilization (22.1 ± 3.3 vs. 18.5 ± 3.6 min, P < 0.001). Complications occurred in 3.3% (CB-2) and 6.2% (RF) of patients with no significant different (p = 0.307). The length of stay after ablation was shorter, but the costs were higher in the CB-2 group (1.94 vs. 2.53 days, P < 0.001 and 91,132.6 ± 3723.5 vs. 81,149.4 ± 6824.1 CNY, P < 0.001) compared to the RF group. Additionally, the rate of early recurrence of atrial arrhythmia (ERAA) was lower in the CB-2 group (14.2 vs. 23.3%, P = 0.047), but the long-term success rate was similar between two groups. CB-2 is associated with shorter procedure time, left atrial dwell time, and length of stay after ablation, as well as lower ERAA, but its costs and fluoroscopy time are greater than the RF group. Moreover, the rate of complications and long-term success is similar between the two groups.