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The negative cost difference between the claims of INA-CBGs and hospital costs for patients which the member of National Health Insurance (JKN) with surgical cases at Jombang Islamic Hospital in 2017 reached IDR -248,095,186. It was hypothesized that the negative cost difference occurred due to the scheduling delay of the surgery and the patients length of stay. The objectives of this research were to identify the factors which affect the negative cost difference in the appendicitis cases. This was an observational analytic research with cross-sectional study design. This research involved 40 medical records of patients who were diagnosed with appendicitis in Jombang Islamic Hospital from January-December 2018. The patients were selected using stratified random sampling. The data were analyzed using linear regression. This research showed that length of stay (β=0.290; p=0.005) and schedule for the surgery (β=0.265; p=0.010) had a significant impact on the negative cost differences in the JKN patient with appendicitis. This research concludes an increase in the length of stay and the delay of the surgery schedule will increase the negative cost difference. Therefore, the hospital should monitor the surgeon compliance toward the length of stay and prevent the delay of surgical schedule in appendicitis cases to reduce the negative cost difference in Jombang Islamic Hospital.