The scenario for engineering education is changing by the effect of theoretical developments in recent years. Appropriate usage of computer technology gives great opportunity to follow these changes and provides student achievement. This paper presents FGATool, a Matlab based interface developed to take role in fractional order system analysis education. Fractional order calculus can be an unfamiliar concept for students, thus it is an indisputable fact that some analysis tools will be useful in the education process. The tool is experienced in classes of master students and the outcomes are recorded. Two main modules of FGATool are presented with their mathematical background all over the paper. Analysis of fractional order systems with fixed and uncertain parameters separately can be realized without complicated technical background. FGATool is also thought to be useful with its user-friendly interface.