The conversion of CO2 into carbon feedstock via CO2 hydrogenation to methane requires a stable catalyst for reaction at high temperatures. Zeolite NaY (abbreviated hereafter as NaY) synthesized from naturally occurring kaolin provides a stable support for Ni nanoparticles. Kaolin can be further dealuminated using sulfuric acid to reduce the Si/Al ratio, but the presence of the remaining sulfur is detrimental to the formation of NaY. The objective of the present study was to synthesize NaY from dealuminated metakaolin, using a method that minimizes the detrimental effects of sulfur, and to investigate the effect of its activity on CO2 methanation. Kaolin from Bangka Belitung, Indonesia, was calcined at 720°C for 4 h to form metakaolin (M) and subsequently treated with sulfuric acid to form dealuminated metakaolin (DM). Excess sulfur was removed by washing with deionized water at 80°C. Zeolite NaY was then synthesized from the M and DM via a hydrothermal method; the relationship between morphology, structural properties, and the catalytic activity of NaY was determined for CO2 methanation at 200–500°C. The presence of excess sulfur following dealumination of metakaolin produced NaY with small surface area and porosity. After Ni impregnation, the synthesized NaY exhibited significant catalytic activity and stability for the reaction at 250–500°C. Analysis by scanning electron microscopy and high-resolution transmission electron microscopy showed the formation of well-defined octahedral structures and large surface areas of ~500 m2/g when NaY was synthesized using DM. Catalytic activity indicated significant conversion of CO2 (67%) and CH4 selectivity (94%) of Ni/NaY from DM in contrast to only 47% of CO2 conversion with 77% of CH4 selectivity for Ni/NaY synthesized from M. Dealuminated metakaolin also produced robust NaY, which indicated no deactivation at 500°C. The combination of well-defined crystallite structures, large surface area, and small Al contents in NaY synthesized from DM helped in CO2 conversion and CH4 selectivity for the reaction at 200–500°C.