Timely diagnosis of group A streptococcal (GAS) sore throat coupled with appropriate antibiotic treatment is necessary to prevent serious post-streptococcal complications, including rheumatic fever (RF) and rheumatic heart disease (RHD). Traditional medicine (TM) is a known common adjunct to formal medical care in sub-Saharan Africa. A better understanding of health-seeking behavior for sore throat both within and outside the formal medical system is critical to improving primary prevention efforts of RF and RHD. A prospective mixed-methods study on the use of TM for sore throat was embedded within a larger epidemiological study of RF in Northern Uganda. Children presenting with symptoms of RF were interviewed about recent TM use as well as health services use for sore throat. One hundred children with a median age of 10 years (interquartile range: 6.8-13 years) completed the TM interview with their parent/guardian as part of a research study of RF. Seventeen, or 17%, accessed a TM provider for sore throat as part of the current illness, and 70% accessed TM for sore throat in the past (73% current or past use). Of the 20 parents who witnessed the TM visit, 100% reported use of crude tonsillectomy. Penicillin was the most frequently prescribed medication by TM providers in 52% of participants who were seen by a TM provider. The use of TM among children presenting with symptoms of sore throat in northern Uganda is common and frequently used in tandem with diagnostic services offered through the formal healthcare system. Engagement with TM practitioners may provide an important avenue for designing effective primary prevention and management strategies of RF and reduce the global burden of RHD.