Background: The definition of late-onset bacterial sepsis (LOS) in very preterm infants is not unified. The objective was to assess the concordance of LOS diagnosis between experts in neonatal infection and international classifications and to evaluate the potential impact on heart rate variability and rate of “bronchopulmonary dysplasia or death”. Methods: A retrospective (2017–2020) multicenter study including hospitalized infants born before 31 weeks of gestation with intention to treat at least 5-days with antibiotics was performed. LOS was classified as “certain or probable” or “doubtful” independently by five experts and according to four international classifications with concordance assessed by Fleiss’s kappa test. Results: LOS was suspected at seven days (IQR: 5–11) of life in 48 infants. Following expert classification, 36 of them (75%) were considered as “certain or probable” (kappa = 0.41). Following international classification, this number varied from 13 to 46 (kappa = −0.08). Using the expert classification, “bronchopulmonary dysplasia or death” occurred less frequently in the doubtful group (25% vs. 78%, p < 0.001). Differences existed in HRV changes between the two groups. Conclusion: The definition of LOS is not consensual with a low international and moderate inter-observer agreement. This affects the evaluation of associated organ dysfunction and prognosis.