Atrial flutter (AFL) is a common arrhythmia with two significant mechanisms, namely, focal (FAFL) and macroreentry (MAFL). Discrimination of the AFL mechanism through noninvasive techniques can improve radiofrequency ablation efficacy. This study aims to differentiate the AFL mechanism using a 12-lead surface electrocardiogram. P-P interval series variability is hypothesized to be different in FAFL and MAFL and may be useful for discrimination. 12-lead ECG signals were collected from 46 patients with known AFL mechanisms. Features for a proposed classifier are extracted through descriptive statistics of the interval series. On the other hand, the class ratio of MAFL and FAFL was 41 : 5, respectively, which was highly imbalanced. To resolve this, different data augmentation techniques (SMOTE, modified-SMOTE, and smoothed-bootstrap) have been applied on the interval series to generate synthetic interval series and minimize imbalance. Modification is introduced in the classic SMOTE technique (modified-SMOTE) to properly produce data samples from the original distribution. The characteristics of modified-SMOTE are found closer to the original dataset than the other two techniques based on the four validation criteria. The performance of the proposed model has been evaluated by three linear classifiers, namely, linear discriminant analysis (LDA), logistic regression (LOG), and support vector machine (SVM). Filter and wrapper methods have been used for selecting relevant features. The best average performance was achieved at 400% augmentation of the FAFL interval series (90.24% sensitivity, 49.50% specificity, and 76.88% accuracy) in the LOG classifier. The variation of consecutive P-wave intervals has been shown as an effective concept that differentiates FAFL from MAFL through the 12-lead surface ECG.