The limitation of the GPS in urban canyon has led to the rapid development of Wi-Fi positioning system (WPS). The fingerprint-based WPS could be divided into calibration and positioning stages. In calibration stage, several grid points (GPs) are selected, and their position tags and featured access points (APs) are collected to build fingerprint database. In positioning stage, real time measurement of APs are compared with the feature of each GP in the database. The k weighted nearest neighbors (KWNN) algorithm is used as pattern matching algorithm to estimate the final positioning result. However, the performance of outdoor fingerprint-based WPS is not good enough for pedestrian navigation. The main challenge is to build a robust fingerprint database. The received number of APs in outdoor environments has large variation. In addition, positioning result estimated by GPS receiver is used as position tag of each GP to automatically build the fingerprint database. This paper studies the lifecycle of fingerprint database in outdoor environment. We also shows that using long time collected data to build database could improve the positioning accuracy. Moreover, a new 3D-GNSS (3D building models aided GNSS) positioning method is used to provide accurate position tags. In this paper, the fingerprint-based WPS has been developed in an outdoor environment near the center of Tokyo city. The proposed WPS can achieve around 17 meters positioning accuracy in urban canyon.