This study provides a comprehensive overview of methodological aspects when using heart rate variability (HRV) measures in educational research. Following PRISMA 2020 guidelines, we searched four databases for relevant studies published until March 5, 2024. From the 48 studies reviewed, we extracted data across three analytical categories: (1) area of study interest and participant populations, (2) data collection and analysis methodologies, and (3) the concurrent and predictive validity of HRV measurement for educational research. Study quality was evaluated using QualSyst assessment criteria. Most studies measured stress and enlisted undergraduate students as participants. Data were predominately collected using wearable devices, measuring HRV for durations of less than 30 min, and in varied contexts, including during exams, while learning, and in experiments. The parameters analyzed varied within both time and frequency domains. HRV data had a moderate level of concurrent validity as a measure of stress in an educational context. The concurrent validity of HRV data for measuring attention remains uncertain with insufficient evidence. Limited correlations appeared between stress and performance. The findings, potentials, and limitations of HRV measures are discussed, and synthesized recommendations for educational research using HRV data are provided.