The unbalanced vehicle growth with the availability of road space is one the causes of traffic congestion. Congestion is often occured on urban roads which are located at the center of the activities. The city of Yogyakarta as a student city and tourism destination has a big influence on increasing of vehicles that have an impact on the environment by the presence of vehicle emissions as a contributor to air pollution. The intersection of Yogyakarta Adisucipto Airport has high traffic volume which is potentially causing traffic congestion. Therefore this study aims to analyze the intersection performance using the MKJI 1997 regulation and Vissim 11.00-08 student version modeling as comparison. The results of study on working days at 06.00-18.00 showed that the peak hour was occurred in the period of 07.00 - 08.00. The Vissim modeling resulted the existing condition at the 07.00 - 08.00 time period was very bad with the level of service F, an average delay of 102.04 second per vehicle, the maximum queue length value at 249.61 m, and the average queue length at 169.54 m. Existing air pollution is indicated by emissions of carbon monoxide (CO) 680.79 gram, nitrogen oxides (NOx) 132.46 gram, and volatile organic compounds (VOC) 157.78 gram. Fuel consumption at the intersection of Yogyakarta's Adisucipto Airport is 9.74 US liquid gallons or equivalent to 2.57 liters. The results of the MKJI 1997 analysis using Vissim showed different values of LOS, delay, and queue length. The analysis using Vissim is better than MKJI 1997 because Vissim can model vehicles and traffic appropriately so it can reduce queue length and delay at the Adisucipto Airport intersection in Yogyakarta.