BACKGROUND: Premature infants may present with damage to the autonomic nervous system (ANS), which may be related to poorer neurological development. Among the techniques used to evaluate the ANS, heart rate variability (HRV) emerged as a simple, non-invasive, and easy to apply tool. The aim of the present study was to analyze and compare HRV in preterm infants at different times of hospitalization in order to verify the possible environmental relationships or clinical evolution with HRV. METHODS: A longitudinal, prospective, and descriptive study with non-probabilistic sampling composed of 25 collections of preterm infants of HRV at two moments: moment I (within 15 days of birth) and moment II (after 45 days post-birth). The Polar V800 heart rate monitor was used with the Polar H10 cardiac transducer to collect HRV, which was collected in the supine position for 15 min. The HRV data were analyzed by the linear method in frequency domain and time domain and by the nonlinear method using Kubios HRV analysis software, version 3.0.2. RESULTS: There was an increase in HRV values at moment II, these being statistically significant in the SD1, ApEn, and SampEn. Data related to increased sympathetic nervous system activity, parasympathetic nervous system activity, and increased index complexity. CONCLUSIONS: The data demonstrate an increase in HRV values in premature infants at moment II, demonstrating a possible development in the maturation of the ANS during hospitalization. TRIAL REGISTRATION: RBR-3x7gz8 retrospectively registered.