In this paper, an operator-based robust nonlinear multivariable tracking control for a manipulator with uncertainties is proposed by using a robust right coprime factorization approach. In general, there exist unknown modelling errors in measuring structural parameters of the manipulator and external disturbances in real situations. In the present control system design, the effect of the modelling errors and disturbance on system performance is considered to be uncertainties in the manipulator dynamics. Considering the uncertainties, an operator-based robust nonlinear multivariable tracking control using robust right coprime factorization is studied. That is, firstly a robustly stable control based on robust right coprime factorization is designed. Secondly, a robust nonlinear multivariable tracking system is proposed for improving the trajectory of the manipulator, and the output tracking performance is evaluated based on the exponential iteration theorem. Finally, the effectiveness of the designed system is confirmed by simulation results.