This paper presents a discrete-time based approach for frequency modulated charge pumps with synchronized controller. In order to handle the varying frequency, this paper first introduced a method to calculate the output voltage of an open-loop charge pump with predefined frequencies, which is improved from a fixed frequency open-loop model verified in previous research. Then a closed-loop model is proposed for synchronized frequency controllers. An algorithm is hence created from the closed-loop model to simulate the output of charge pumps. The simulation result shows a competitive accuracy and much faster speed when comparing it with transistor level simulations. Overall, this paper demonstrated its value in terms of modeling the frequency modulated charge pumps and hence assisted the top-down design flow.