Although the popularity of flywheel (FW) devices in sports research is increasing, to date, no study has been designed to test the reliability of electromyographic (EMG) variables during FW squats as a basic lower-body FW resistance exercise. At the primary level, our study was conducted to determine the minimum number of the consecutive flywheel (FW) squat repetitions that need to be averaged in a single set to obtain excellent reliability of peak, mean and three position-specific EMG variables. At the secondary level, comprehensive analysis for peak and mean EMG variables was done. Intra-set reliability was investigated using the minimum number of repetitions determined from the primary level of the study. Twenty-six participants performed five sets of seven squats with three FW loads (0.05, 0.125, 0.225 kg∙m2). EMG signals were collected from eight leg muscles. By averaging twelve consecutive repetitions, we obtained ICC2.k > 0.95 for mean and peak EMGRMS regardless of the muscle, load or phase of the squat (concentric vs. eccentric). Due to the heterogeneity of the results at the primary level, position-specific variables were excluded from the inter-set reliability analysis at the secondary level. Trustworthy mean and peak EMG variables from the primary level showed good to excellent inter-set reliability. We suggest averaging twelve consecutive squat repetitions to achieve good to excellent intra-session reliability of EMG variables. By following the proposed protocol, activation of leg muscles can be confidently studied in intra-session repeated-measures study designs.