In this study, the effects of the induced magnetic field on the separation of drugs with different structures and polarities were investigated. Herein, column chromatography within an induced magnetic field was introduced to examine the influence of magnetic fields on materials and their interactions. For this purpose, the drugs were categorized into three series based on polarity: tramadol (logP 1.34) and heroin (logP 1.58) as the polar series; cocaine (logP 2.3) and noscapine (logP 2.58) as the moderate polarity series; and papaverine (logP 3.00) and ketamine (logP 3.21) as the non-polar series. A magnetic field with different intensities and orientations was induced in the solenoid by applying an electric current. It was observed that the pressure within the chromatographic column decreases as the induced magnetic field intensity increases, eventually stabilizing. This behavior can be explained by the magnetic field effect on the mobile phase polarity and viscosity, which offers an approach for gradient elution in reversed-phase chromatography by employing the magnetic field without changing the mobile phase composition. Alternatively, increasing the induced magnetic field resulted in greater shifts in retention times, allowing drugs to be detected more rapidly. Other effects of the magnetic field on separation were changes in peak widths and resolutions. The results indicated that drugs with moderate polarity were most influenced by the induced magnetic field.