Background and Objectives: Kidney transplant recipients are more vulnerable to respiratory viral infections because of immunosuppressive therapy. Given the clinical overlap between SARS-CoV-2, influenza virus, and human respiratory syncytial virus (HRSV), simultaneous molecular testing may support timely clinical decision-making. This study aimed to determine the prevalence of these viruses among hospitalized adult kidney transplant recipients with acute respiratory infection. Methods: This cross-sectional study was conducted from November 2023 to January/February 2025 (corresponding to Aban 1402 to Bahman 1403 in the Persian calendar) at Shahid Dr. Labbafinejad Hospital, Tehran, Iran. Convenience sampling was performed among hospitalized adult kidney transplant recipients with acute respiratory infection, mainly during autumn, winter, and spring. Respiratory samples were tested for SARS-CoV-2, influenza virus, and HRSV using multiplex real-time RT-PCR, and demographic, clinical, and laboratory data were collected. Results: The mean age was 45.16 ± 14.33 years (95% CI: 43–48years). SARS_CoV_2 was detected in 18 cases (12.8%), influenza virus in 13 cases (9.2%), and HRSV in one case (0.7%). No viral co-infection was recorded in the available laboratory dataset. Conclusion: SARS-CoV-2 and influenza virus were the dominant respiratory viruses among hospitalized adult kidney transplant recipients with acute respiratory infection, whereas HRSV was uncommon. Multiplex real-time RT-PCR may be a valuable diagnostic strategy in transplant centers, although larger multicenter studies with full seasonal coverage are needed.