Heart rate (HR) has been shown to be a robust autonomic measure of emotional reactivity. However, there are discrepancies in the analytical approaches applied, which leads to difficulties in the comparison of results between studies. Also, the choice of different analytical approaches does not always respond to differences in research questions. At present, two predominant approaches are employed: a synchronous approach (e.g. pre vs. post-intervention) and a longitudinal approach, which analyzes the differences in HR trajectories throughout a task. The objective of this work is to describe and compare the profiles of autonomic reactivity to an emotional modulation task according to the two paradigms of analysis most prevalent in the current psychophysiological literature. To do that, a sample of 44 children aged 5 was constituted and their HR was recorded throughout the viewing of a video with different emotional content. HR was analyzed under the two approaches mentioned above. Under the synchronous approach, no differences were found between HR according to emotional modulation. However, the longitudinal analysis showed statistically significant differences between the conditions. Due to the temporal characteristics of emotional processes, it does not seem sufficient to compare HR between a point before and a point after an emotional induction. The results suggest the importance of considering analytical methodologies according to the complexity of the phenomenon studied.