This study aimed to evaluate factors that may predispose patients to not adhere to prescribed medication after endoscopic sinus surgery (ESS) and to compare SNOT-22 scores at 0–12 months post-operatively between adherent and non-adherent patients. CRS patients who underwent ESS between 2012 and 2016 were recruited to this retrospective cohort study. Adherence was assessed through a questionnaire and review of medical notes. Ninety-four participants were included (61% male, mean age 60). Of those, 66% did not adhere to their prescribed post-operative CRS medication timing or dosage. The most common reason for non-adherence was improvement of symptoms (17%), followed by deterioration of symptoms (11%) and side effects (10%). Post-operative SNOT-22 scores were lowest for non-intentionally non-adherent (NINA) participants with a mean of 10.5 [95% CI: 7.47–13.5], compared to 25.0 for intentionally non-adherent (INA) [95% CI: 17.6–32.4] and 17.7 for adherent patients [95% CI: 13.7–21.7], p = 0.01. This study identifies that almost two-thirds of patients are not compliant with CRS medications after ESS. NINA participants reported lower post-operative SNOT-22 scores compared to INA and adherent participants. Future studies should focus on educating patients to continue with medications post-operatively despite an initial improvement in symptoms.