Deposition of scale layers inside pipelines leads to many problems, e.g., reducing the internal diameter of pipelines, damage to drilling equipment because of corrosion, increasing energy consumption because of decreased efficiency of equipment, and shortened life, etc., in the petroleum industry. Gamma attenuation could be implemented as a non-invasive approach suitable for determining the mineral scale layer. In this paper, an intelligent system for metering the scale layer thickness independently of each phase’s volume fraction in an annular three-phase flow is presented. The approach is based on the use of a combination of an RBF neural network and a dual-energy radiation detection system. Photo peaks of 241Am and 133Ba registered in the two transmitted detectors, and scale-layer thickness of the pipe were considered as the network’s input and output, respectively. The architecture of the presented network was optimized using a trial-and-error method. The regression diagrams for the testing set were plotted, which demonstrate the precision of the system as well as correction. The MAE and RMSE of the presented system were 0.07 and 0.09, respectively. This novel metering system in three-phase flows could be a promising and practical tool in the oil, chemical, and petrochemical industries.