The paper considers a discrete state-space model for transients in a three-level flying capacitor DC-DC converter. A transition matrix is obtained for a Pulse Width Modulation (PWM) period. The matrix elements are expanded into a power series using a selected small parameter. The matrix eigenvalues that determine the natural balancing dynamics transients are presented in the form of power series as well. Four separate transients are constructed based on four possible PWM period initial states (topologies). Inductor current and capacitor voltage transients are found for the voltage source power-up as the arithmetic average of the four separate transients. The discrete solutions are replaced by continuous ones. The resulting transients that are elementary functions of the circuit parameters, PWM period, and voltage reference demonstrate good agreement with the simulation results.