ObjectivesRetrograde Cricopharyngeal Dysfunction (RCPD) is treated by botulinum toxin (BTX) injection into the cricopharyngeus. This prospective study compares the effectiveness and side effects of operating room (OR) and in‐office (IO) injections.MethodsPatients over 18 years of age with inability to burp, abdominal, thoracic, or cervical gurgling sounds, bloating, and excessive flatulence were diagnosed with RCPD and included in the study. Injections were performed in the OR (80U) or IO (30U) by the senior author. An RCPD questionnaire quantifying major and minor symptoms on a Likert scale, Eating Assessment Tool‐10 (EAT‐10), and Generalized Anxiety Score−7 (GAD‐7), were completed preinjection; at 1, 2, and 3 weeks; and 3 months postoperatively. Linear mixed models were used to analyze effects of BTX injection on RCPD symptoms, the EAT‐10, and the GAD‐7.Results108 (55 M/53F) patients completed the pretreatment survey, 53 (31 OR vs. 22 IO) completed the 3‐week follow‐up, and 36 (22 OR vs. 14 IO) completed the 3‐month questionnaire. Average posttreatment RCPD scores were significantly lower in both groups at 3 weeks and 3 months (p < 0.0001), There was no difference between IO or OR (p = 0.4924). GAD‐7 scores were significantly lower in both groups at week 3 (p = 0.0018) and month 3 (p = 0.0012). Postinjection EAT‐10 scores were significantly higher in OR compared with IO (p = 0.0379).ConclusionOR and IO injections are equally effective in the treatment of RCPD. Postinjection dysphagia is more severe after the OR injections which may be related to higher doses of BTX used. General anxiety levels decrease with treatment.Level of Evidence2 Laryngoscope, 2024