Pharyngitis and tonsillitis are the most common acute respiratory infections (ARIs) in children aged ≤5 years. The analysis of published data showed that some probiotics could decrease the frequency and number of days with ARIs. This study evaluated the safety and efficacy of Limosilactobacillus reuteri ATCC PTA 5289 and DSM 17938 to reduce the duration and severity of ARI symptoms. This randomised controlled trial included children aged from 6 months to 5 years, with pharyngitis or tonsillitis, who were randomised to receive a probiotic product containing L. reuteri ATCC PTA 5289 and L. reuteri DSM 17938 or placebo, as drops, ingested orally for 10 days as adjuvants to the use of non-steroidal anti-inflammatory drugs. The main outcomes were the duration and severity of ARI symptoms. The secondary outcomes were changes in salivary immunoglobulin A and inflammatory biomarkers. There was no fever on day 2 and subsequent days in the L. reuteri group (37.3 ±0.5 °C vs 38.6±0.3 °C, P<0.05). Beginning on day 3, the severity of sore throat (5±0.9 vs 8±1.2, P<0.05) was lower in the L. reuteri group. Significant differences in the days with runny nose, nasal congestion, days of non-programmed visits to the medical office or emergency department, levels in tumoral necrosis factor-alpha (TNF-alpha) and related costs of treatment were observed in the L. reuteri group. The frequency of adverse events was similar between the groups. Therefore, L. reuteri ATCC PTA 5289 combined with L. reuteri DSM 17938 is a safe and effective adjunct to reduce the symptoms of pharyngitis or tonsillitis in children.