Background: Septic arthritis is a potentially debilitating condition in young infants, and the optimal duration of antimicrobial therapy to prevent complications remains a clinical dilemma. This study compared long-term outcomes of short and long courses of parenteral antimicrobial s and identified predictors of unfavorable outcomes in infants with septic arthritis. Methods: This randomized controlled trial was conducted at the Department of Paediatrics, Dhaka Shishu Hospital, Bangladesh, from July 2021 to June 2023. Sixty-nine infants aged 0–2 months with septic arthritis were randomized into two groups: Group A received long-term parenteral antimicrobial treatment (14 days) and Group B received short-term antimicrobial treatment (7 days). Data were collected using purposive sampling. Patients were followed up at 3, 6, and 12 months. Variables included clinical improvement, radiological recovery, haematological parameters, and complications. Statistical analysis used SPSS v26, with significance at p < 0.05. Results: Group A included 35 participants and Group B 34 participants. Follow-up attrition occurred in both groups. At 3 months, 83.9% of Group A and 78.6% of Group B showed clinical improvement (p=0.602). Radiological recovery at 6 months was similar between groups (89.7% vs. 92.3%, p=0.999). After 12 months, 85.2% of Group A and 80.0% of Group B had favorable outcomes (p=0.722). Predictors of unfavorable outcomes included delayed treatment initiation and polyarticular involvement. Conclusion: Short- and long-term antimicrobial therapies showed comparable outcomes in infants with septic arthritis. The duration of antimicrobial therapy did not significantly affect long-term complications, suggesting that a shorter course may be sufficient in most cases.