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Background: Little is known about the recent trends in antibiotic and phytopharmaceutical prescribing for acute upper (URIs) and lower respiratory tract infections (LRIs) in children and adolescents. Therefore, this study investigated changes in the prescription of antibiotics and phytopharmaceuticals in children diagnosed with acute URIs and LRIs in pediatric practices in Germany in 2013, 2018, and 2022. Methods: The present retrospective study included children aged 2–12 years diagnosed with acute URIs or LRIs in one of 180 pediatric practices in 2013, 2018, and 2022. The URIs included nasopharyngitis, sinusitis, pharyngitis, tonsillitis, laryngitis and tracheitis, and upper respiratory infections of multiple and unspecified sites, while the LRIs corresponded to bronchitis. The primary outcomes were the proportion of children being prescribed antibiotics and the proportion of those being prescribed phytopharmaceuticals. Results: A total of 120,894 children were diagnosed with acute URIs or LRIs in 2013 compared to 116,844 in 2018 and 127,821 in 2022. The prevalence of antibiotic prescription decreased for all diagnoses between 2013 and 2022. This decrease was statistically significant for both 2013–2018 and 2018–2022 for nasopharyngitis, pharyngitis, and bronchitis. Meanwhile, there was a significant increase in the use of phytopharmaceuticals for all diagnoses between 2013 and 2018. The prevalence of phytopharmaceutical prescription decreased slightly between 2018 and 2022, but this decrease was generally not statistically significant. Conclusions: The prescription of antibiotics has decreased and that of phytopharmaceuticals has increased in children diagnosed with acute URIs and LRIs in Germany over the last decade. More data are needed to corroborate these findings in other settings.