A fast method to simultaneously calibrate multiple MEMS Magnetic Inertial Measurement Units (MIMUs) accurately in the field is needed in many application areas. The MEMS MIMUs require calibration of systematic errors of bias, sensitivity, non-orthogonality and misalignment, which vary with temperature and use. Even after calibration, the sensors undergo stochastic errors in static and dynamic conditions and thus uncertainty of output must also be modeled. We propose a method for easy and fast calibration of multiple MIMUs together, while mounted on a single platform. The precise alignment of sensors is not assumed. Our method calibrates both fixed array of MEMS MIMUs or many independent MIMUs simultaneously using kinematic constraints. The novelty of our approach is that the uncertainty of sensors output is also learned as part of our model. Compared with existing state-of-art methods, our algorithm gives more consistent readings of all MIMUs and our framework also predicts the associated uncertainty of the sensor output. The uncertainty prediction of individual sensors is particularly helpful in the sensor fusion.