The aim of this study was to determine the waiting times in a primary care clinic in the military hospital in the capital city of Saudi Arabia and their impact on self-medication by patients. We performed this nested case-control study from a cross-sectional study involving self-medication with antibiotics at a primary care clinic in the Riyadh Military Hospital. From the cross-sectional study, 289 returned questionnaires were selected to implement the nested study. Both the perceived and the actual waiting times showed significant independent association with the practice of antibiotic self-medication (SMA) with OR 3.64 (CI 2.20-6.00) and 2.44 (CI 1.49-3.99), respectively. Community pharmacies were found to be by far the most common source of antibiotics (85%). The most common ailments for which participants self-medicated were the common cold (67.9%), sore throat (65.5 %) and chest infection (31.5%). The most frequent reason for practicing self-medication with antibiotics was the long waiting time to see a doctor. Prior experience of antibiotic use resulted in SMA in 40.7% of cases and considering the illness not serious enough for consultation with a doctor resulted in SMA in 38.9% of cases. Knowledge about the ineffectiveness of antibiotics for viral infections was significantly higher among patients who were not practicing SMA (p=0.018). However, there was no significant difference in awareness about antibiotic resistance between patients who were practicing self-medication and those who were not. Interventions aimed at preventing self-medication should include reducing both the actual and the perceived waiting time in primary care clinics (PCC). The high prevalence of self- medication with antibiotics at Riyadh Military Hospital PCC indicates that appropriate interventions are required to decrease improper antibiotic use, which may also help in the prevention of antibiotic resistance.