As a rare malignant tumor, cervical neuroendocrine cancer (NEC) is difficult in diagnosis even for experienced pathologists. A computer-assisted diagnosis may be helpful for the improvement of diagnostic accuracy. Nevertheless, the computer-aided pathological diagnosis has to face a great challenge that the hundred-million-pixels or even gig-pixels whole slide images (WSIs) cannot be applied directly in the existing deep convolution network for training and analysis. Therefore, the construction of a neural network to realize the automatic screening of cervical NEC is challenging; meanwhile, as far as we know, little attention has been paid to this field. In order to address this problem, here we present a multiple-instance learning method for automatic recognition of cervical NEC on pathological WSI, which consists of the Sliding Detector module and Lesion Analyzer module. A pathological WSI dataset, which is composed of 84 NEC cases and 216 NEC-free cases from the Pathological Department of West China Second University Hospital, is applied to evaluate the performance of the method. The experimental results show that the recall rate, accuracy rate, and precision rate of our method for automatic recognition are 92.9%, 92.7%, and 83.0%, respectively, demonstrating the effectiveness and the potential in clinical practice. The application of this method in computer-assisted pathological diagnosis is expected to decrease the misdiagnosis as well as the false diagnosis of rare cervical NEC, and, consequently, improve the therapeutic effect of cervical cancers.