Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen responsible for many nosocomial infections. It is quite resistant to various antibiotics, caused by the absence of general diffusion pores in the outer membrane. Instead, it contains many substrate-specific channels. Among them are the two phosphate- and pyrophosphate-specific porins OprP and OprO. Phosphonic acid antibiotics such as fosfomycin and fosmidomycin seem to be good candidates for using these channels to enter P. aeruginosa bacteria. Here, we investigated the permeation of fosfomycin through OprP and OprO using electrophysiology and molecular dynamics (MD) simulations. The results were compared to those of the fosmidomycin translocation, for which additional MD simulations were performed. In the electrophysiological approach, we noticed a higher binding affinity of fosfomycin than of fosmidomycin to OprP and OprO. In MD simulations, the ladder of arginine residues and the cluster of lysine residues play an important role in the permeation of fosfomycin through the OprP and OprO channels. Molecular details on the permeation of fosfomycin through OprP and OprO channels were derived from MD simulations and compared to those of fosmidomycin translocation. In summary, this study demonstrates that the selectivity of membrane channels can be employed to improve the permeation of antibiotics into Gram-negative bacteria and especially into resistant P. aeruginosa strains.