We assessed the effectiveness of lyophilised banked human milk as a fortifier to feed very-low-birth-weight infants (VLBWIs). This study aimed to evaluate the safety and tolerability of human milk (HM) with HM lyophilisate as an additive compared to the standard additive (cow’s milk protein). In this Phase I double-blind randomised controlled clinical trial, set in the intensive and intermediate care units of a tertiary hospital, 40 very-low-birth-weight infants were enrolled and allocated into two groups: HM plus HM lyophilisate (LioNeo) or HM plus commercial additive (HMCA). The inclusion criteria were preterm infants, birth weight 750–1500 g, small or adequate for gestational age, exclusively receiving donor HM, volume ≥ 100 mL/kg/day, and haemodynamically stable. Participants were followed up for 21 consecutive days. The primary outcome measures were necrotising enterocolitis (NEC), late-onset sepsis (LOS), death, gastrointestinal bleeding or perforation, diarrhoea, regurgitation, vomiting, and abdominal distension. The LioNeo and HMCA groups had similar weights at baseline. The regression models showed no differences between the groups in terms of the primary outcomes. Diarrhoea, gastrointestinal perforation, NEC, and LOS were absent in the LioNeo group (1 LOS and 1 NEC in the HMCA group). Multiple regression analysis with the total volume of milk as a covariate did not show significant differences. The lyophilisation of donor HM was considered safe and tolerable for use in stable haemodynamically VLBWIs.