Abstract This work analyzes the minimum tollbooth problem in atomic network congestion games with unsplittable flows. The goal is to place tolls on edges, such that there exists a pure Nash equilibrium in the tolled game that is a social optimum in the untolled one. Additionally, we require the number of tolled edges to be the minimum. This problem has been extensively studied in non-atomic games, however, to the best of our knowledge, it has not been considered for atomic games before. By a reduction from the weighted CNF SAT problem, we show both the NP-hardness of the problem and the W[2]-hardness when parameterizing the problem with the number of tolled edges. On the positive side, we present a polynomial time algorithm for networks on series-parallel graphs that turns any given state of the untolled game into a pure Nash equilibrium of the tolled game with the minimum number of tolled edges.