In the last decade, small unmanned aerial vehicles (UAVs/drones) have become increasingly popular in the airborne observation of large areas for many purposes, such as the monitoring of agricultural areas, the tracking of wild animals in their natural habitats, and the counting of livestock. Coupled with deep learning, they allow for automatic image processing and recognition. The aim of this work was to detect and count the deer population in northwestern Serbia from such images using deep neural networks, a tedious process that otherwise requires a lot of time and effort. In this paper, we present and compare the performance of several state-of-the-art network architectures, trained on a manually annotated set of images, and use it to predict the presence of objects in the rest of the dataset. We implemented three versions of the You Only Look Once (YOLO) architecture and a Single Shot Multibox Detector (SSD) to detect deer in a dense forest environment and measured their performance based on mean average precision (mAP), precision, recall, and F1 score. Moreover, we also evaluated the models based on their real-time performance. The results showed that the selected models were able to detect deer with a mean average precision of up to 70.45% and a confidence score of up to a 99%. The highest precision was achieved by the fourth version of YOLO with 86%, as well as the highest recall value of 75%. Its compressed version achieved slightly lower results, with 83% mAP in its best case, but it demonstrated four times better real-time performance. The counting function was applied on the best-performing models, providing us with the exact distribution of deer over all images. Yolov4 obtained an error of 8.3% in counting, while Yolov4-tiny mistook 12 deer, which accounted for an error of 7.1%.