The immune system is subject to all sorts of influences. Pain is one of them, accompanying an organism’s existence. It is essential to be aware of and account for age-related characteristics of the innate immunity in order to adequately assess their dynamics in ontogenesis. The literature is scarce on the changes to the killing activity of neutrophils occurring in newborns in response to acute pain. The aim of this study was to detect potential changes to the phagocytic activity of neutrophils in response to an algogenic stimulus in newborn rats. The experiments were carried out in 3-5-day-old rats. Two groups were formed: the control group and the main group, in which acute pain was modelled. Blood samples were collected 2, 30–60 and 120–180 minutes after exposure to the algogenic stimulus. The microbicidal activity of neutrophils was measured using a spectrophotometric modification of the spontaneous/stimulated nitroblue tetrazolium (NBT) reduction test. The results were compared using the Mann-Whitney U test. In the first hour following pain modeling, the stimulated NBT reduction test demonstrated an increase in the measured parameters from 71.5 to 87.4 a.u. (р < 0.001); the spontaneous NBT reduction test showed an increase from 50.7 to 58.6 a.u. (p < 0.01) 30 to 60 min after exposure. The most pronounced change of the microbicidal activity coefficient was observed 2 min after pain modeling, increasing from 1.40 to 1.72 a.u (р < 0.001). By the end of the experiment, the measured parameters approximated their initial values. During the analysis, we accounted for the fact that the neutrophil response to the algogenic stimulus was unfolding in the setting of microbial colonization occurring in newborns.