Abstract This paper presents a robust occupancy analysis system for thermal imaging. Reliable detection of people is very hard in crowded scenes, due to occlusions and segmentation problems. We therefore propose a framework that optimises the occupancy analysis over long periods by including information on the transition in occupancy, when people enter or leave the monitored area. In stable periods, with no activity close to the borders, people are detected and counted which contributes to a weighted histogram. When activity close to the border is detected, local tracking is applied in order to identify a crossing. After a full sequence, the number of people during all periods are estimated using a probabilistic graph search optimisation. The system is tested on a total of 51,000 frames, captured in sports arenas. The mean error for a 30-minute period containing 3-13 people is 4.44 %, which is a half of the error percentage optained by detection only, and better than the results of comparable work. The framework is also tested on a public available dataset from an outdoor scene, which proves the generality of the method.