The separation of CO2/CH4 using porous carbon can be increased by the presence of a functional group of nitrogen on the carbon surface. This study explores the potential of porous carbon derived from the palm kernel shell (C-PKS) impregnated with a deep eutectic solvent (DES), which is one of the chemicals containing a nitrogen element. The DES was composed of a quaternary ammonium salt of choline chloride (ChCl) and a hydrogen bond donor of alcohol. Three alcohols of 1-butanol (-ol), ethylene glycol (-diol), and glycerol (-triol) were employed to study the effects of a number of hydroxyl groups in the separation performance. The research steps included (i) the preparation of DES-impregnated porous carbon synthesized from the palm kernel shell (DES/C-PKS), (ii) characterization of the material, and (ii) a separation test of CO2/CH4 with a breakthrough system. Materials were characterized using scanning electron microscopy (SEM) combined with energy-dispersive X-ray spectroscopy (EDX), N2-sorption analysis, and Fourier transform infrared (FTIR) spectroscopy. SEM images showed a significant morphological difference of pristine carbon and DES/C-PKS. There was a significant decrease in the range of 67–73% of a specific surface area with respect to pristine carbon, having initially 800 m2/g. However, the N element on the carbon surface increased after impregnation treatment, which was shown from the intensity of the FTIR graphs and EDX analysis. Adsorption isotherm revealed that DES/C-PKS could enhance up to 1.6 times the adsorption capacity of CO2 at 1 atm and 30 °C while increasing the selectivity of CO2/CH4 up to 125%. The breakthrough experiment showed that all DES/C-PKS materials displayed a better performance for the separation of CO2/CH4, indicated by a longer breakthrough time and enhancement of CO2 uptake. The best separation performance was achieved by DES/C-PKS using glycerol as a hydrogen bond donor with 15.4 mg/g of CO2 uptake or equivalent to 95% enhancement of the uptake capacity compared to pristine porous carbon. Also, the cycling test revealed that DES/C-PKS can be used repetitively, which further highlights the efficiency of the material for the separation of CO2/CH4.