Thromboembolism and bleeding complications remain a major limitation of the catheter ablation (CA) for atrial fibrillation (AF). This study aimed to evaluate the association between achieving target activated clotting time (ACT) and clinical factors, and to develop an appropriate protocol for early achievement of target ACT in patients with direct oral anticoagulants (DOACs). At the initiation cohort, 190 patients (127 males, age 68 ± 9) taking DOACs who underwent CA for AF were studied. All patients underwent transthoracic echocardiography/transesophageal echocardiography/blood sampling before the CA. The ACTs were measured before heparin administration (pre-ACT) and in 30 min (30-min ACT) after initial heparin administration (100 U/kg +3000 U). At the validation cohort, the indicator obtained from the first study was reassessed in the subsequent 138 patients (94 males, age 68 ± 10). At the initiation cohort, 30-min ACT reached the target ACT in 79/190 patients (42%). Univariate analysis showed that longer pre-ACT, elevated aPTT, higher PT-INR, antiplatelet medication, and dabigatran were associated with achieving the target 30-min ACT. On multivariate analysis, only longer pre-ACT was independently associated with achieving the target 30-min ACT (P = 0.0396, the optimal cutoff value; 130 s). As a novel protocol, we added 2000 U of initial heparin dose (total 100 U/kg +5000 U) in patients with low pre-ACT (< 130); then, the achievement rate to target 30-min ACT improved from 41.6 to 80.5% without increasing bleeding complications. Our novel protocol of initial heparin administration based on pre-ACT is useful for an appropriate systemic anticoagulation in patients taking DOACs during the CA for AF.