We consider stochastic and open quantum systems with a finite number of states, where a stochastic transition between two specific states is monitored by a detector. The long-time counting statistics of the observed realizations of the transition, parametrized by cumulants, is the only available information about the system. We present an analytical method for reconstructing generators of the time evolution of the system compatible with the observations. The practicality of the reconstruction method is demonstrated by the examples of a laser-driven atom and the kinetics of enzyme-catalyzed reactions. Moreover, we propose cumulant-based criteria for testing the non-classicality and non-Markovianity of the time evolution, and lower bounds for the system dimension. Our analytical results rely on the close connection between the cumulants of the counting statistics and the characteristic polynomial of the generator, which takes the role of a cumulant generating function. © 2014 IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.