A systems modelling approach can be used to describe and optimise responses to training stimuli within individuals. However, the requirement for regular maximal performance testing has precluded the widespread implementation of such modelling approaches in team-sport settings. Heart rate variability (HRV) can be used to measure an athlete’s adaptation to training load, without disrupting the training process. As such, the aim of the current study was to assess whether chronic HRV responses, as a representative marker of training adaptation, could be predicted from the training loads undertaken by elite Rugby Sevens players. Eight international male players were followed prospectively throughout an eight-week pre-season period, with HRV and training loads (session-RPE [sRPE] and high-speed distance [HSD]) recorded daily. The Banister model was used to estimate vagally-mediated chronic HRV responses to training loads over the first four weeks (tuning dataset); these estimates were then used to predict chronic HRV responses in the subsequent four-week period (validation dataset). Across the tuning dataset, high correlations were observed between modelled and recorded HRV for both sRPE (r = 0.66 ± 0.32) and HSD measures (r = 0.69 ± 0.12). Across the sRPE validation dataset, seven of the eight athletes met the criterion for validity (typical error <3% and Pearson r >0.30), compared to one athlete in the HSD validation dataset. The sRPE validation data produced likely lower mean bias values, and most likely higher Pearson correlations, compared to the HSD validation dataset. These data suggest that a systems theory approach can be used to accurately model chronic HRV responses to internal training loads within elite Rugby Sevens players, which may be useful for optimising the training process on an individual basis.