This study was conducted to evaluate observed runoff data collected every 10 minutes at stream gauging stations in Jeju Island using a physically-based model, SWAT. The Hancheon watershed was selected as study area, and ephemeral stream algorithm suggested by previous research was incorporated into the model, which is able to simulate ephemeral runoff pattern of Jeju streams. Simulated runoff and runoff rates were compared to observations during 2008-2013, which showed ‘very good’ performance rating in Nash-Sutcliffe model efficiency (ME) and determination coefficient (R²). Some observations had problems such that runoff rates were very high for some rainfall events with little amount of antecedent rainfall, and were very low or missing with much rainfall comparing to previous researches. Additionally, regression equation between precipitation and simulated runoff was generated with high degree of correlation. The equation can be utilized to simply predict reasonable runoff, or to investigate and complement the abnormal or missing data of observations on the assumption that modelling results were sufficiently reliable and satisfactory. As results, minimizing the error in calibrating the model by evaluation of observed data would be helpful to accurately model the rainfall-runoff characteristics and analyze the water balance components of watersheds in Jeju Island.