Background: Percutaneous closure of secundum atrial septal defects (ASDs) under only transesophageal echocardiogram (TEE) guidance is less invasive and avoids exposure to radiation, but the treatment of choice is controversial. Methods: One hundred and forty-four patients with a secundum ASD were included in this study. The patients received percutaneous device closure (PCDC/TEE) (n = 74) or peratrial device closure (PDC/TEE) (n = 70). A double-disk ASD occluder was used in both groups. The treatment was performed under only TEE guidance in both groups. Physical exams, electrocardiography, and echocardiography were performed immediately after device release, and at discharge, 3, 6, 12 months, and at yearly intervals after the procedure. Results: In ASD with a maximum diameter less than 20 mm, the successful closure rate was 100% for all PCDC/TEE and PDC/TEE. When the ASD diameter was between 20 mm and 25 mm, the success rate was 84% for PCDC/TEE and 100% for PDC/TEE. The average intracardiac manipulation time was 19.4 ± 6.4 minutes for PCDC/TEE and 5.7 ± 7.0 minutes for PDC/TEE (p < 0.001). The average procedure time was 23.1 ± 6.8 minutes for PCDC/TEE and 51.1 ± 8.2 minutes for PDC/TEE (p < 0.001). The postoperative hospital stay was 3 ± 1 days for PCDC/TEE and 5 ± 1 days for PDC/TEE (p < 0.001). For the mean follow-up of 520 ± 256 days, there no cardiac deaths or significant residual shunts were documented in either group. Conclusions: In patients with an ASD less than 25 mm, PCDC/TEE is a safe and effective method of ASD closure. Additionally, PCDC/TEE is less traumatic, provides better cosmetic results, and decreases hospital stays. However, when the ASD diameter is greater than 20 mm and the aortic rim of ASD is less than 3 mm, the peratrial approach may be a better choice.