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Background: The overuse and inappropriate prescribing of antibiotics in early childhood remains a global public health concern, mainly due to the risk of accelerating antimicrobial resistance (AMR). During and after the COVID-19 pandemic, primary care services in Kosovo underwent notable changes in prescribing practices. Aim: This study aimed to examine the prescribing rate and patterns of antibiotic prescribing among children aged 1–7 years in primary health care centers in Prishtina and Ferizaj between January 2022 and January 2025, and to compare regional differences in prescribing behaviors. Methods: A retrospective observational study was conducted using data from the national electronic health record system. All pediatric visits for children aged 1–7 years were included. Antibiotic prescriptions linked to infectious diagnoses were analyzed. Descriptive statistics, Chi-square tests, and multivariable logistic regression were applied to evaluate prescribing prevalence, regional differences, and associated factors. Results: Out of 4,320 pediatric visits, antibiotics were prescribed in 1,328 cases (30.7%). Prevalence was significantly higher in Ferizaj (34.2%) than in Prishtina (28.5%, p < 0.01). Amoxicillin–clavulanic acid (42.9%) and amoxicillin (21.5%) were the most prescribed antibiotics. Metronidazole accounted for 16.4% of prescriptions, while Ferizaj showed a significantly higher use of macrolides (11.7% vs. 6.2%) and cephalosporins (7.9% vs. 3.4%). Only 61.4% of prescriptions were consistent with international clinical guidelines. Younger age (1–3 years), winter season, and residence in Ferizaj were independently associated with higher odds of antibiotic prescribing. Conclusions: Antibiotic prescribing among Kosovar children aged 1–7 years remains high, with concerning regional differences and suboptimal adherence to clinical guidelines. These findings underline the urgent need for standardized pediatric prescribing protocols, enhanced physician education, and robust antibiotic stewardship programs in Kosovo’s primary care system.