Abstract Background and objective The automated detection of atrial activations (AAs) recorded from intracardiac electrograms (IEGMs) during atrial fibrillation (AF) is challenging considering their various amplitudes, morphologies and cycle length. Activation time estimation is further complicated by the constant changes in the IEGM active zones in complex and/or fractionated signals. We propose a new method which provides reliable automatic extraction of intracardiac AAs recorded within the pulmonary veins during AF and an accurate estimation of their local activation times. Methods First, two recently developed algorithms were evaluated and optimized on 118 recordings of pulmonary vein IEGM taken from 35 patients undergoing ablation of persistent AF. The adaptive mathematical morphology algorithm (AMM) uses an adaptive structuring element to extract AAs based on their morphological features. The relative-energy algorithm (Rel-En) uses short- and long-term energies to enhance and detect the AAs in the IEGM signals. Second, following the AA extraction, the signal amplitude was weighted using statistics of the AA sequences in order to reduce over- and undersensing of the algorithms. The detection capacity of our algorithms was compared with manually annotated activations and with two previously developed algorithms based on the Teager–Kaiser energy operator and the AF cycle length iteration, respectively. Finally, a method based on the barycenter was developed to reduce artificial variations in the activation annotations of complex IEGM signals. Results The best detection was achieved using Rel-En, yielding a false negative rate of 0.76% and a false positive rate of only 0.12% (total error rate 0.88%) against expert annotation. The post-processing further reduced the total error rate of the Rel-En algorithm by 70% (yielding to a final total error rate of 0.28%). Conclusion The proposed method shows reliable detection and robust temporal annotation of AAs recorded within pulmonary veins in AF. The method has low computational cost and high robustness for automatic detection of AAs, which makes it a suitable approach for online use in a procedural context.