Experimental software datasets describing software projects in terms of their complexity and development time have been the subject of intensive modeling. A number of various modeling methodologies and modeling designs have been proposed including such approaches as neural networks, fuzzy, and fuzzy neural network models. In this study, we introduce the concept of the Rule-based fuzzy polynomial neural networks (RFPNN) as a hybrid modeling architecture and discuss its comprehensive design methodology. The development of the RFPNN dwells on the technologies of Computational Intelligence (CI), namely fuzzy sets, neural networks, and genetic algorithms. The architecture of the RFPNN results from a synergistic usage of RFNN and PNN. RFNN contribute to the formation of the premise part of the rule-based structure of the RFPNN. The consequence part of the RFPNN is designed using PNN. We discuss two kinds of RFPNN architectures and propose a comprehensive learning algorithm. In particular, it is shown that this network exhibits a dynamic structure. The experimental results include well-known software data such as the NASA dataset concerning software cost estimation and the one describing software modules of the Medical Imaging System (MIS).