In the past decades, the number of in vitro fertilization (IVF) procedures for the conception of a child has been rising continuously, however, the success rate of artificial insemination remained low. According to current statistics, large portion of unsuccessful IVF relates to some women' factors. As the directly related female organ, the proper investigation of the uterus has primary importance. Namely, visible markers may indicate inflammations or other negative effects that jeopardize successful implantation. The purpose of this study is to support the observability of the uterus from this aspect by providing computer-aided tools for the extraction of its wall from video hysteroscopy. As for methodology, fully convolutional neural networks (FCNNs) are used for the automatic segmentation of the video frames to determine the region of interest. We provide the necessary steps for the applicability of the general deep learning framework for this specific task. Moreover, we increase segmentation accuracy with applying ensemble-based approaches at two levels. First, the predictions of a given FCNN are aggregated for the overlapping regions of subimages, which are derived from the splitting of the original images. Next, the segmentation results of different FCNNs are fused via a weighted combination model; optimization for adjusting the weights are also provided. Based on our experimental results, we have achieved 91.56% segmentation accuracy regarding the recognition of the uterus wall.