Background. One important ingredient for many applications of nuclear physics to astrophysics, nuclear energy, and stockpile stewardship are cross sections for reactions of neutrons with rare isotopes. Since direct measurements are often not feasible, indirect methods, e.g. (d,p) reactions, should be used. Those (d,p) reactions may be viewed as three-body reactions and described with Faddeev techniques. Purpose. Faddeev equations in momentum space have a long tradition of utilizing separable interactions in order to arrive at sets of coupled integral equations in one variable. Optical potentials representing the effective interactions in the neutron (proton) nucleus subsystem are usually non-Hermitian as well as energy-dependent. Potential matrix elements as well as transition matrix elements calculated with them must fulfill the reciprocity theorem. The purpose of this paper is to introduce a separable, energy-dependent representation of complex, energy-dependent optical potentials that fulfill reciprocity exactly. Results. Starting from a separable, energy-independent representation of global optical potentials based on a generalization of the Ernst-Shakin-Thaler (EST) scheme, a further generalization is needed to take into account the energy dependence. Applications to n$+^{48}$Ca, n$+^{208}$Pb, and p$+^{208}$Pb are investigated for energies from 0 to 50~MeV with special emphasis on fulfilling reciprocity. Conclusions. We find that the energy-dependent separable representation of complex, energy-dependent phenomenological optical potentials fulfills reciprocity exactly. In addition, taking into account the explicit energy dependence slightly improves the description of the $S$ matrix elements.