The adequate characterization of pain is critical in diagnosis and therapy selection, and currently is subjectively assessed by patient communication and self-evaluation. Thus, pain recognition and assessment have been a target of study in past years due to the importance of objective measurement. The goal of this work is the analysis of the electrocardiogram (ECG) under emotional contexts and reasoning on the physiological classification of pain under neutral and fear conditions. Using data from both contexts for pain classification, a balanced accuracy of up to 97.4% was obtained. Using an emotionally independent approach and using data from one emotional context to learn pain and data from the other to evaluate the models, a balanced accuracy of up to 97.7% was reached. These similar results seem to support that the physiological response to pain was maintained despite the different emotional contexts. Attempting a participant-independent approach for pain classification and using a leave-one-out cross-validation strategy, data from the fear context were used to train pain classification models, and data from the neutral context were used to evaluate the performance, achieving a balanced accuracy of up to 94.9%. Moreover, across the different learning strategies, Random Forest outperformed the remaining models. These results show the feasibility of identifying pain through physiological characteristics of the ECG response despite the presence of autonomic nervous system perturbations.