Flow is defined as a psychological state characterized by becoming deeply absorbed in a task, losing track of time, and diminished self-awareness. Flow research typically involves associating physiological data recorded during a task with subsequently completed questionnaires (i.e., post-task reports). This approach is limited due to the temporal mismatch between the continuously recorded physiological data and the post-task reports of flow. We introduce a novel method that enables the continuous, real-time measurement of perceived flow. Participants continuously indicated their perceived degree of flow in real time by pressing a custom-made foot pedal while engaging in a flow-inducing task (playing the video game Thumper in virtual reality), and electrocardiogram (ECG) signals were recorded as a physiological measure. In the first experiment, participants played the game under two conditions, one with the pedal and one without as a baseline. After each condition, they completed the validated Flow Short Scale (FSS). The second experiment included an extended 40-minute gameplay session with performance measurements. Our results suggest that interacting with the pedal did not interfere with the flow experience nor did it alter heart rate variability (Experiment 1). Moreover, the pedal measurement provided a reliable continuous self-assessment of flow, as indicated by correlations between real-time and post-task flow ratings (Experiments 1 and 2). Overall, our findings confirm that the proposed method enables the assessment of the temporal evolution of flow and the accompanying physiological markers.