Although the effectiveness of probiotics has only been proven in specific conditions, their use in children is massively widespread because of their perception as harmless products. Recent evidence raises concerns about probiotics' safety, especially but not only in the paediatric population due to severe opportunistic infections after their use. This review aimed at summarising available case reports on invasive infections related to probiotics' use in children. For this purpose, we assessed three electronic databases to identify papers describing paediatric patients with documented probiotic-derived invasive infections, with no language restrictions. A total of 49 case reports from 1995 to June 2021 were identified. The infections were caused by Lactobacillus spp. (35%), Saccharomyces spp. (29%), Bifidobacterium spp. (31%), Bacillus clausii (4%), and Escherichia coli (2%). Most (80%) patients were younger than 2 years old and sepsis was the most observed condition (69.4%). All the patients except one had at least one condition facilitating the development of invasive infection, with prematurity (55%) and intravenous catheter use (51%) being the most frequent. Three (6%) children died. Given the large use of probiotics, further studies aiming at evaluating the real incidence of probiotic-associated systemic infections are warranted.