Yogyakarta is a city whose development is quite rapid, this has an impact on the increasingly congested traffic flow, especially at the crossroads that often occur congestion. Like the Senopati intersection in Yogyakarta, traffic jams often occur at rush hour. The use of phase sequences in the APILL system still uses a clockwise phase sequence. This study aims to analyze the performance of intersections after the change of phase sequence of APILL lamp using VISSIM software. The data used in this research is using traffic survey method and other supporting data (environmental condition, road geometric) in field and modeling using VISSIM 10.0 program. Based on the modeling results can be known intersection performance on the existing condition is at service level F and the value of delay 115.5 seconds / vehicle. After several scenarios are carried out, an effective phase sequence is obtained when the turn ratio at the intersection reaches 90% for the right turn ratio and 10% for the straight and east arm ratio with a delay value of 70.29 seconds / vehicle and service level E.