The objective of this study was to assess the impact of an alimentary integrator composed of spirulina (Spirulina platensis; SP), produced at the Centre Médical St Camille of Ouagadougou, Burkina Faso, on the nutritional status of undernourished HIV-infected and HIV-negative children. We compared two groups of children: 84 were HIV-infected and 86 were HIV-negative. The duration of the study was 8 weeks. Anthropometric and haematological parameters allowed us to appreciate both the nutritional and biological effect of SP supplement to traditional meals. Rehabilitation with SP shows on average a weight gain of 15 and 25 g/day in HIV-infected and HIV-negative children, respectively. The level of anaemia decreased during the study in all children, but recuperation was less efficient among HIV-infected children. In fact 81.8% of HIV-negative undernourished children recuperated as opposed to 63.6% of HIV-infected children (Z: 1.70 (95% CI -0.366, -0.002, p = 0.088)). Our results confirm that SP is a good food supplement for undernourished children. In particular, rehabilitation with SP also seems to correct anaemia and weight loss in HIV-infected children, and even more quickly in HIV-negative undernourished children.