Unmanned Aerial Vehicles (UAVs) represent easy, affordable, and simple solutions for many tasks, including the collection of traffic data. The main aim of this study is to propose a new, low-cost framework for the determination of highly accurate traffic flow parameters. The proposed framework consists of four segments: terrain survey, image processing, vehicle detection, and collection of traffic flow parameters. The testing phase of the framework was done on the Zagreb bypass motorway. A significant part of this study is the integration of the state-of-the-art pre-trained Faster Region-based Convolutional Neural Network (Faster R-CNN) for vehicle detection. Moreover, the study includes detailed explanations about vehicle speed estimation based on the calculation of the Mean Absolute Percentage Error (MAPE). Faster R-CNN was pre-trained on Common Objects in COntext (COCO) images dataset, fine-tuned on 160 images, and tested on 40 images. A dual-frequency Global Navigation Satellite System (GNSS) receiver was used for the determination of spatial resolution. This approach to data collection enables extraction of trajectories for an individual vehicle, which consequently provides a method for microscopic traffic flow parameters in detail analysis. As an example, the trajectories of two vehicles were extracted and the comparison of the driver’s behavior was given by speed—time, speed—space, and space—time diagrams.