Cell phones with GPS function as well as GPS loggers are widely used and users' geographic information can be easily obtained. However, still battery consumption in these mobile devices is main concern and then obtaining GPS positioning data so frequently is not allowed. In this paper, a stayed location estimation method for sparse GPS positioning information is proposed. After generating initial clusters from a sequence of measured positions, the effective radius is set for every cluster based on positioning accuracy and the clusters are merged effectively using it. After that, short-time clusters are removed temporarily but measured positions included in them are not removed. Then the clusters are merged again, taking all the measured positions into consideration. This process is performed twice, in other words, two-stage short-time cluster removal is performed, and finally accurate stayed location estimation is realized even when the GPS positioning interval is five minutes or more. Experiments demonstrate that the total distance error between the estimated stayed location and the true stayed location is reduced by more than 33% and also the proposed method much improves F₁ measure compared to conventional state-of-the-art methods.