The article presents model for evaluation of virtual team performance based on the intelligent methods of Multi-level fuzzy rules and Fuzzy Signature. The hierarchical system of parameters for virtual team performance evaluation is elaborated by applying expert survey. The aggregated measure of performance of virtual project team is derived from twelve parameters assigned to three categories (team, task and interaction). The experimental research is based on fuzzy analysis of interaction data of virtual teams which worked on implementation of three software solution projects. The research results provide evidence for the feasibility of using the proposed method as the tool for virtual project managers seeking to improve their leadership techniques, and to derive parameters for performance evaluation based on intelligent computing methods.