Background Surgical Site Infections are a major cause of morbidity and mortality among operated patients. In spite of the accessibility of universal and national guidelines for surgical prophylaxis, recent studies surveying the present routine of prophylaxis have demonstrated overutilization of a wide range antibacterial medication for a single patient. Few studies have shown qualitatively factors influencing this and perceptions of surgeons on surgical antibiotic prophylaxis use. Unfortunately, none of these studies have been done in Tanzania. Objective To describe the perceptions of surgeons on surgical antibiotic prophylaxis use at an urban tertiary hospital. Methods A qualitative study involving in-depth interviews with surgeons was conducted in English by the primary investigator. The interviews were audio-recorded and transcribed verbatim. Systematic text condensation by Malterud was used for data analysis. Findings Fourteen surgeons and obstetrics and gynaecologists participated. Their perceptions were summarized into three main categories: Inadequate data to support practice; one who sees the patient decides the antibiotic prophylaxis; prolonged antibiotic use for fear of unknown. The participants perceived that choice of antibiotic should be based on local hospital data for bacterial resistance pattern, however the hospital guidelines and data for surgical site infection rates are unknown. Fear of getting infection and anticipating complications led to prolonged antibiotics use. Conclusion The study provides an understanding of surgical antibiotic prophylaxis use and its implementation challenges. This was partly expressed by unavailability of local data and guidelines to enhance practice. To improve this, there is a need of guidelines that incorporates local resistance surveillance data and enhanced antibiotic stewardship programmes. A strong consideration should be placed into ways to combat the fears of surgeons for complications, as these significantly affect the current practise with use of surgical antibiotic prophylaxis.