Rotating charged black strings are exact solutions of four-dimensional Einstein–Maxwell equations with a negative cosmological constant and a non-trivial spacetime topology. According to the AdS/CFT correspondence, these black strings are dual to rotating thermal states of a strongly interacting quantum field theory with nonzero chemical potential that lives in a cylinder. The dynamics of linear fluctuations in the dual field theory can be studied from the perturbation equations for classical fields in a black-string spacetime. With this motivation in mind, we develop here a completely gauge and tetrad invariant perturbation approach to deal with the gravitoelectromagnetic fluctuations of rotating charged black strings in the presence of sources. As usual, for any charged black hole, a perturbation in the background electromagnetic field induces a metric perturbation and vice versa. In spite of this coupling and the non-vanishing angular momentum, we show that linearization of equations of the Newman–Penrose formalism leads to four separated second-order complex equations for suitable combinations of the spin coefficients, the Weyl and the Maxwell scalars. Then, we generalize the Chandrasekhar transformation theory by the inclusion of sources and apply it to reduce the perturbation problem to four decoupled inhomogeneous wave equations—a pair for each sector of perturbations. The radial part of such wave equations can be put into Schrödinger-like forms after Fourier transforming them with respect to time. We find that the resulting effective potentials form two pairs of supersymmetric partner potentials and, as a consequence, the fundamental variables of one perturbation sector are related to the variables of the other sector. The relevance of such a symmetry in connection to the AdS/CFT correspondence is discussed, and future applications of the pertubation theory developed here are outlined.