The purpose of this study was to evaluate changes in endurance fitness of elite-level rugby union players (n = 35) undertaking skill-based conditioning games for a 9-week preseason training period. Metabolic conditioning was conducted exclusively in the form of skill-based conditioning games in conjunction with heart rate (HR) telemetry. Two markers of cardiorespiratory fitness were assessed at weekly intervals via the recording of HR responses to an intermittent multistage shuttle test. Significant differences post-training were observed for the percentage of maximal HR (% HRmax) reached during the final test stage and the percentage of HR recovery (% HR recovery) from the end of the final stage to the end of the final 1-minute rest period. Significant improvements were demonstrated for % HR recovery at week 7 (p < 0.05) and week 9 (p < 0.01), and % HRmax in the final test stage was significantly lower at weeks 4, 5, and 7 (p < 0.05) and week 9 (p < 0.01). Further improvements from mid-preseason to the end of the preseason training period were observed for % HR recovery scores in week 8 (p < 0.01) and week 9 (p = 0.012) and for % HRmax reached in the final test stage at week 9 (p < 0.05). These results indicate skill-based conditioning games were successful at improving markers of cardiorespiratory endurance for the duration of a 9-week training period in the elite-level professional rugby union players studied. The HR monitoring was demonstrated to be an effective and practical means of quantifying intensity in the conditioning games format and of tracking changes in cardiorespiratory fitness.