The welfare of crocodiles on commercial farms in southern Africa requires precise assessment, focusing on stocking densities and pen conditions. However, disputes between animal welfare groups and farm owners persist due to inadequate methodologies for quantifying these factors. This study aimed to address these disputes and enhance crocodile welfare assessment by introducing a novel technique using a low-cost consumer uncrewed aerial vehicle (UAV) and open-source photogrammetry software. The objective was to quantify key welfare parameters accurately and efficiently. The study involved applying the UAV-based technique to two large Nile crocodile (Crocodylus niloticus) farms in South Africa. The approach enabled the mapping and surveying of crocodile pens, facilitating the determination of stocking densities, biomass indicators, and other pen-related attributes. Comparisons were made between UAV-derived crocodile counts and farmer estimates. The UAV-based crocodile counts significantly differed from the estimates provided by farmers, underscoring the need for a more precise assessment method. The technique's cost-effectiveness was evident, with implementation expenses totalling less than R10 000, a fraction of the cost associated with commercial UAV surveys. The introduced UAV-based technique offers a valuable solution to the ongoing debates regarding crocodile welfare on commercial farms. By quantifying key parameters accurately and economically, it empowers farmers and animal welfare groups to make informed decisions. The method's ease of adoption, demonstrated through its use by some Southern African crocodile farmers, signifies its potential for widespread application, ultimately contributing to improved crocodile welfare.