One method for on-line fault detection in synchronous generator is stator current harmonics analysis. In this paper, the flexible neural network with reconstruction structure during learning has been used to evaluate the stator current harmonics in different loads.Generator modeling, finite element method and state space model make training set of flexible neural network. Many points from generator capability curve are used to complete this set. Flexible neural network that is used in this paper is a perception network with single hidden layer, flexible hidden layer neuron and back propagation algorithms. Results are show that the trained flexible neural network can identify stator current harmonics for desired load from the capability curve. The error is less than 10% in compared to the values obtained directly from the CFE-SS algorithms. The parameters of modeled generator are 43950 (KVA), 11 (kV), 3000 (rpm), 50 (HZ), (PF=0.5).