We study the behavior of the non-adiabatic population transfer between resonances at an exceptional point in the spectrum of the hydrogen atom. It is known that, when the exceptional point is encircled, the system always ends up in the same state, independent of the initial occupation within the two-dimensional subspace spanned by the states coalescing at the exceptional point. We verify this behavior for a realistic quantum system, viz. the hydrogen atom in crossed electric and magnetic fields. It is also shown that the non-adiabatic hypothesis can be violated when resonances in the vicinity are taken into account. In addition, we study the non-adiabatic population transfer in the case of a third-order exceptional point, in which three resonances are involved.