The membrane permeation of weak acids and bases couples to the ambient pH and can be studied using pH-sensitive dyes as reporters. Such fluorescence measurements with aliphatic amine drugs have revealed biexponential kinetics of permeation into liposomes (Eyer et al. J. Controlled Release 2014, 173, 102). Permeability coefficients have been obtained using the faster of the two kinetic components. Here, the origin of the biexponential kinetics is studied with a kinetic rate model that in addition to drug permeation accounts for the protonation of the drug and the dye. Surprisingly, the experimental readout is found to strongly depend on the rates of protonation. The analysis demonstrates that fluorescence studies of drug permeation relying on pH-sensitive proxies should be accompanied by comprehensive modeling of the relevant kinetic processes.