In the context of precision horticulture, decision support tools play a significant role in providing fruit growers with insights into orchard conditions, facilitating informed decisions regarding orchard management practices. This study presents the development of an autonomous yield estimation system designed to provide decision support to small commercial orchards. Autonomous yield estimation is based on the application of UAVs and AI. AI is used to identify and quantify fruitlets and fruits in photographs collected by UAV. In this article, we present our prototype of an autonomous yield estimation system. The adapted “4+1” architecture was applied to design a system with a holistic approach analyzing software, hardware, and ecosystem requirements. Six datasets are presented, which contain the images of fruitlets and fruits of apples, pears, and cherries. Three CNN models were trained: YOLOv8m, YOLOv9m, and YOLOv10m. The experiment showed that the most accurate was YOLOv9m, which achieved mean accuracies of 0.896 mAP@50 and 0.510 mAP@50:95 for all datasets.