Computer vision methods offer great potential for rapid image-based identification of medically important arthropod specimens. However, imaging large numbers of specimens is time consuming, and it is difficult to achieve the high image quality required for machine learning models. Conventional imaging methods for identifying and digitizing arthropods, such as insects and spiders, use a stereomicroscope or macro lenses with a camera. This method is challenging due to the narrow field of view, especially when large numbers of arthropods need to be processed. In this paper, we present a high-throughput scanner-based method for capturing images of arthropods that can be used to generate large datasets suitable for training machine learning algorithms for identification. We demonstrate the ability of this approach to image arthropod samples collected with different sampling methods, such as sticky traps (unbaited, in different colors), baited mosquito traps as used by the US Centers for Disease Control and Prevention (CDC) and BioGents-Sentinel (BGS), and UV light traps with a sticky pad. Using different strategies to place the arthropods on a charge-coupled device (CCD) flatbed scanner and optimized settings that balance processing time and image quality, we captured high-resolution images of various arthropods and obtained morphological details with resolution and magnification similar to a stereomicroscope. We validate the method by comparing the performance of three different deep learning models (InceptionV3, ResNet and MobileNetV2) on two different datasets, namely the scanned images from this study and the images captured with a camera of a stereomicroscope. The results show that the performance of the models trained on the two datasets is not significantly different, indicating that the quality of the scanned images is comparable to that of a stereomicroscope.