The diagnosis of incipient fault is important for power transformer condition monitoring. Incipient faults are monitored by conventional and artificial intelligence based models. Key gases, percentage value of gases, and ratio of the Doernenburg, Roger, IEC methods are input variables to artificial intelligence models, which affects the accuracy of incipient fault diagnosis, so selection of the most influencing relevant input variable is an important research area. With this main objective, Waikato Environment for Knowledge Analysis software is applied to 360 simulated samples having different operating lives to find the most influencing input parameters for incipient fault diagnosis in the gene expression programming model. The Waikato Environment for Knowledge Analysis identifies%C2H2,%C2H4,%CH4, C2H6/C2H2, C2H2/C2H4, CH4/H2, C2H4/C2H6, and C2H2/CH4 as the most relevant input variables in incipient fault diagnosis, and it is used for fault diagnosis using different artificial intelligence methods, i.e., artificial neural networks, fuzzy logic, support vector machines, and gene expression programming. The compared results shows that gene expression programming gives better results than the artificial neural network, fuzzy logic, and support vector machine with accuracy variation from 98.15 to 100%, proving the gene expression programming method can be used in transformer fault diagnosis research.