Trigger finger is a common hand disease, causing swelling, painful popping and clicking in moving the affected finger joint. To better evaluate patients with trigger finger, segmentation of flexor tendons from magnetic resonance (MR) images of finger joints, which can offer detailed structural information of tendons to clinicians, is essential. This paper presents a novel model-based method with three stages for automatically segmenting the flexor tendons. In the first stage, a set of tendon contour models (TCMs) is initialized from the most proximal cross-sectional image via two-step ellipse estimation. Each of the TCMs is then propagated to its distally adjacent image by affine registration. The propagation is sequentially performed along the proximal-distal direction until the most distal image is reached, as the second stage of segmentation. The TCMs on each cross-sectional image are refined in the last stage with the snake deformation. MR volumes of three subjects were used to validate the segmentation accuracy. Compared with the manual results, our method showed good accuracy with small average margins of errors (within 0.5 mm) and large overlapping ratio (dice similarity coefficient above 0.8). Overall, the proposed method has great potential for morphological change assessment of flexor tendons and pulley-tendon system modeling for image guided surgery.