The aim of this study was to analyze the effects of HRV-guided training compared to a standardized prescription on i) time to complete 5-km running performance (t5km), ii) peak treadmill running speed (Vpeak) and its time limit (tlim at Vpeak), and iii) autonomic cardiac modulation (i.e., parasympathetic activity and recovery) in untrained women. Additionally, we correlated changes in t5km with changes in Vpeak, tlim at Vpeak and autonomic cardiac modulation. Thirty-six untrained women were divided into a HRV-guided training group (HRVG) and a control group (CG). The CG followed a pre-defined program, alternating moderate-intensity continuous training (MICT) and high-intensity interval training (HIIT). The determination of MICT or HIIT was based on the pre-training HRV for HRVG. MICT was performed if HRV was < mean – 1 SD of previous measures. Otherwise, HIIT was prescribed. The t5km, Vpeak, tlim at Vpeak, parasympathetic activity (i.e., rMSSD) and parasympathetic reactivation (i.e., HRR) were measured before and after the training period. The t5km decreased to a greater magnitude in the HRVG (-17.5±5.6% vs. -14±4.7%; Effect Size (ES) between-group difference=moderate). rMSSD and tlim at Vpeak only improved in HRVG (+23.3±27.8% and +23.6±31.9%, respectively). The HRVG experienced greater improvements in Vpeak and HRR (Vpeak: 10±7.3% vs. 8.2±4.7%; HRR: 19.1±28.1% vs. 12.6±12.9%; ES between-group difference=small). Although HRVG performed less MICT than CG, the volume of MICT was negatively related to changes in t5km. Vpeak changes were highly correlated with t5km changes. The greater improvements in HRVG for t5km and autonomic modulation reinforce the potential application of this tool.