Endometrial thickness is closely related to gyneco-logical function and is an important biomarker in transvaginal ultrasound (TVUS) examinations for assessing female reproductive health. Manual measurement is time-consuming and subject to high inter- and intra- observer variability. In this paper, we present a fully automated endometrial thickness measurement method using deep learning. Our pipeline consists of: 1) endometrium segmentation using a VGG-based U-Net, and 2) endometrial thickness estimation using medial axis transformation. We conducted experimental studies on 137 2D TVUS cases (74/63 secretory phase/proliferative phase). On a test set of 27 cases/277 images, the segmentation Dice score is 0.83. For thickness measurement, we achieved mean absolute error of 1.23/1.38 mm and root mean squared error of 1.79/1.85 mm on two different test sets. The results are considered well within the clinically acceptable range of ±2 mm. Furthermore, our phase-stratified analysis shows that the measurement variance from the secretory phase is higher than that from the proliferative phase, largely due to the high variability of the endometrium appearance in the secretory phase. Future work will extend our current algorithm toward different clinical outcomes for a broader spectrum of clinical applications.