The aims of this study were to compare the reliability and magnitude of jump height between the two standard procedures of analysing force platform data to estimate jump height (take-off velocity [TOV] and flight time [FT]) in the loaded squat jump (SJ) exercise performed with a free-weight barbell and in a Smith machine. Twenty-three collegiate men (age 23.1 ± 3.2 years, body mass 74.7 ± 7.3 kg, height 177.1 ± 7.0 cm) were tested twice for each SJ type (free-weight barbell and Smith machine) with 17, 30, 45, 60, and 75 kg loads. No substantial differences in reliability were observed between the TOV (Coefficient of variation [CV]: 9.88%; Intraclass correlation coefficient [ICC]: 0.82) and FT (CV: 8.68%; ICC: 0.88) procedures (CV ratio: 1.14), while the Smith SJ (CV: 7.74%; ICC: 0.87) revealed a higher reliability than the free-weight SJ (CV: 9.88%; ICC: 0.81) (CV ratio: 1.28). The TOV procedure provided higher magnitudes of jump height than the FT procedure for the loaded Smith machine SJ (systematic bias: 2.64 cm; P<0.05), while no significant differences between the TOV and FT procedures were observed in the free-weight SJ exercise (systematic bias: 0.26 cm; P>0.05). Heteroscedasticity of the errors was observed for the Smith machine SJ (r2: 0.177) with increasing differences in favour of the TOV procedure for the trials with lower jump height (i.e. higher external loads). Based on these results the use of a Smith machine in conjunction with the FT more accurately determine jump height during the loaded SJ.