Csikszentmihalyi's concept of the "flow state" was initially discovered in experts deeply engaged in self-rewarding activities. However, recent neurophysiology research often measures flow in constrained and unfamiliar activities. In this perspective article, we address the challenging yet necessary considerations for studying flow state's neurophysiology. We aggregate an activity-autonomy framework with several testable hypotheses to induce flow, expanding the traditional "challenge skill balance" paradigm. Further, we review and synthesise the best methodological practices from neurophysiological flow studies into a practical 24-item checklist. This checklist offers detailed guidelines for ensuring consistent reporting, personalising and testing isolated challenge types, factoring in participant skills, motivation, and individual differences, and processing self-report data. We argue for a cohesive approach in neurophysiological studies to capture a consistent representation of flow states.