Cancer progression can be described by continuous-time Markov chains whose state space grows exponentially in the number of somatic mutations. The age of a tumor at diagnosis is typically unknown. Therefore, the quantity of interest is the time-marginal distribution over all possible genotypes of tumors, defined as the transient distribution integrated over an exponentially distributed observation time. It can be obtained as the solution of a large linear system. However, the sheer size of this system renders classical solvers infeasible. We consider Markov chains whose transition rates are separable functions, allowing for an efficient low-rank tensor representation of the linear system’s operator. Thus we can reduce the computational complexity from exponential to linear. We derive a convergent iterative method using low-rank formats whose result satisfies the normalization constraint of a distribution. We also perform numerical experiments illustrating that the marginal distribution is well approximated with low rank.