Background: In sporting and combat settings, optimal fluid replacement is rarely achieved, exacerbating physiological strain. It is unknown if prescribed fluid replacement following exercise in heat impacts heart rate variability (HRV). Purpose: Compare prescribed drinking (PD) and ad libitum (AL) fluid replacement on HRV following exercise in heat. Methods: Twelve participants (26 ± 5 years, VO2max: 58.44 ± 7.05 mL·kg−1·min−1) completed three trials in heat (36 °C, 36% humidity) on separate days, and were placed into groups, PD or AL. Recovery was assessed ~24 h later (hydration and HRV). HRV time and frequency was measured using a 3-lead electrocardiogram. Two-way repeated measures analysis of variance measured changes in HRV pre-trial, post-trial, and follow-up between groups. Data reported: p-value, mean difference (MD). Results: Fluid consumption was greater in PD during recovery (p = 0.012, MD = 1245 mL). Both groups were euhydrated at follow-up. HRV time (p < 0.001, MD = 24.23) and frequency (p < 0.001, MD = −1.98 ms2) decreased post-trial and increased by follow-up (time, p < 0.001, MD = −32.12; frequency, p < 0.001, MD = 2.38 ms2). HRV was similar between groups (p > 0.05). Conclusions: Replacing ≥60% fluid sufficiently rehydrates and restores HRV 24 h post-exercise in heat and mild dehydration (BML ≤ 3%). Prescribed fluid consumption during recovery was ~30% greater. Additional measures of recovery sensitive to heat strain may provide a more holistic understanding of specific mechanisms of recovery.