Abstract Background Recurrent respiratory infections (RRIs) are defined by the presence of at least one of the following criteria: (i) > 6 annual respiratory infections (RIs); (ii) > 1 monthly RIs involving the upper airways from September to April; (iii) > 3 annual RIs involving the lower airways represent a very common health problem in the first years of life. We conducted a multi-centre, prospective, single-open study to assess the efficacy and the safety of Streptococcus salivarius 24SMBc and Streptococcus oralis 89a in the prevention of upper respiratory tract infections (URTIs) in children. Methods Ninety-one children (M:F = 47:44, mean age 7.4 ± 2.3 years) with RRIs were enrolled in the study between September and November 2018. At baseline, children received Streptococcus salivarius 24SMBc and Streptococcus oralis 89a as 2 puffs for nostril twice/day for 7 days/months. The treatment lasted for 3 consecutive months. Efficacy was expressed in terms of absence or presence of fever, cough, bronchospasm, rhinorrhea and otalgia, at 1 month (T1), and 3 (T3) months. Safety and tolerability of the probiotic were evaluated on the basis of the number and type of adverse events (AEs) recorded during the treatment. Results Children treated with Streptococcus salivarius 24SMBc and Streptococcus oralis 89a showed a significant decrease of symptoms including episodes of fever, cough, bronchospasm, rhinorrhea, and otalgia (p < 0.001) compared to baseline. The treatment significantly reduced the number of episodes of fever, cough, bronchospasm, rhinorrhea, otalgia, and cough also in patients with positive familial history for atopy and in atopic children (p < 0.05). No significant differences in symptoms among children with negative familial history for atopy and children with positive familial history for atopy subgroups, not atopic and atopic children subgroups, and smoke-exposed and not smoke-exposed subgroups were observed (p > 0.05). Conducting a subgroup analysis according to the age, it has been reported that children aged 1–3 years old showed an improvement in all symptoms, however, they become statistically significant only at the end of the 3 months of treatment (p < 0.05). Conversely, in children aged 3–6 and 6–12 years old, the therapeutic efficacy was progressive and significant already from the first month of therapy (p < 0.05). None of the children were withdrawn from the study because of AEs, although 9 children experienced burning nose leading to interruption of therapy. Conclusions Our findings suggest that Streptococcus salivarius 24SMBc and Streptococcus oralis 89a treatment is safe and seems to be effective on short-term in the treatment of RRIs. Studies involving a longer observation period are necessary to establish the real efficacy of the product for the treatment of pediatric patients affected by RRIs.