The determination of two imidazoline derivatives [oxymetazoline HCl (OXY) and xylometazoline HCl (XYLO)] was described using different potentiometric platforms. The first electrode type was constructed using tetraphenyl borate (TPB) as anionic exchanger with β-cyclodextrins (β-CD) as ionophore forming oxymetazoline-tetraphenyl borate (OXY-TPB) and xylometazoline-tetraphenyl borate (XYLO-TPB), respectively. The second electrode type was prepared by modification of the first type by conjugation with magnetic iron oxide nanoparticles (MNP) forming (OXY-MNP) and (XYLO-MNP). The synthesized electrodes were fully characterized. The effect of magnetic nano-sized particles as a highly dispersible material with β-CDs on the electrode characteristics was investigated and compared against the classical electrodes. The response time, working pH range and selectivity coefficients were studied. The functionalized nano-electrodes (OXY-MNP and (XYLO-MNP) were found to be more sensitive than the classical electrodes with linearity ranges (1×10−6–1×10−2 M). The functionalized nano-electrodes were successfully applied for the in-line analysis of OXY and XYLO in pharmaceutical dosage forms and spiked rabbit aqueous humor samples with no prior extraction of treatment. This suggests the future use of these electrodes in clinical studies of both drugs of interest.