Background Throat carriage of Streptococcus pyogenes could play a crucial role in the transmission of infection to households and community settings. In Yemen, there is no information about S. pyogenes throat carriage among university students.Aim This study aimed for finding out the rate of asymptomatic throat carriage of Streptococcus pyogenes and its associated risk factors among medical students of Queen Arwa University in Sana’a City, Yemen.Methods This cross-sectional study was conducted at Queen Arwa, between December 2022 to April 2023. A total of 300 throat swabs were randomly collected from medical university students. Streptococcus pyogenes were isolated and identified by using standard bacteriological procedures. Also, the required data were obtained by using the designed questionnaire.Results Out of 300 specimens, 5(1.7%) were positive for S. pyogenes throat carriage. The high rate of S. pyogenes was among females (2%), age group of 25–30 years (8.3%), dental students (3.9%), and who studied at the third level (3.7%). Also, the high rate of the carriage was whose fathers’ are the trading field (3.7%) and mothers as housewives (2%), whose fathers and mothers’ held a university certificate (2.9%) and primary school (6.5%), respectively, with a low income (12.5%), none of their families has a sore throat (2.1%), and a history of hospitalization (3.2%).Conclusion There was a relatively low rate of S. pyogenes throat carriage in healthy medical students compared with international investigations. Standard precautions such as adequate hand and respiratory hygiene and avoiding overcrowded settings are used to prevent and control transmission of GAS infection.