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Patient self-referral is a condition when patients refer themselves to higher level health facilities without having to see anyone else first. Despite the expansion in the number of health facilities, it has been seen when patients routinely accessed referral hospitals without a formal referral. The study aims to evaluate cost of treatment among self-referred outpatients at referral hospitals compared to primary health care facilities. Comparative cross-sectional study design was used and the required sample size for the study was determined by using formula of double populations mean comparison cost of treatment for diseases leading to outpatient visits. A total of 794 participants (397 from referral hospital and 397 from primary health facilities) were included in the study. Data was collected using face-to-face interview from December 1 to 30, 2017. Data entry and analysis were made using SPSS version 20. Descriptive statistics and independent samples t-test were performed. A total of 783 outpatients responded to the interview of the study and 391 of them were from referral hospital and 392 from primary health facilities. The mean of outpatient visit cost per visit for the treatment of diseases leading to outpatient visits was significantly higher at referral hospitals compared to primary health facilities [95% CI=6.13 (5.07-7.18)] USD. The mean cost of outpatient visits for the treatment of all type of diseases leading to outpatient visits was significantly higher at referral hospitals and at least two times of primary level health facilities. Health care providers should create awareness in the community about referral linkages to inform patients and their families the additional costs they incur when they bypass the proximal primary health facilities.