As functional magnetic resonance imaging (fMRI) becomes widely used, the demands for evaluation of fMRI processing pipelines and validation of fMRI analysis results is increasing rapidly. The current NPAIRS package, an IDL-based fMRI processing pipeline evaluation framework, lacks system interoperability and the ability to evaluate general linear model (GLM)-based pipelines using prediction metrics. Thus, it can not fully evaluate fMRI analytical software modules such as FSL.FEAT and NPAIRS.GLM. In order to overcome these limitations, a Java-based fMRI processing pipeline evaluation system was developed. It integrated YALE (a machine learning environment) into Fiswidgets (a fMRI software environment) to obtain system interoperability and applied an algorithm to measure GLM prediction accuracy. The results demonstrated that the system can evaluate fMRI processing pipelines with univariate GLM and multivariate canonical variates analysis (CVA)-based models on real fMRI data based on prediction accuracy (classification accuracy) and statistical parametric image (SPI) reproducibility. In addition, a preliminary study was performed where four fMRI processing pipelines with GLM and CVA modules such as FSL.FEAT and NPAIRS.CVA were evaluated with the system. The results indicated that (1) the system can compare different fMRI processing pipelines with heterogeneous models (NPAIRS.GLM, NPAIRS.CVA and FSL.FEAT) and rank their performance by automatic performance scoring, and (2) the rank of pipeline performance is highly dependent on the preprocessing operations. These results suggest that the system will be of value for the comparison, validation, standardization and optimization of functional neuroimaging software packages and fMRI processing pipelines.