The hydrogen isotopic composition (δ2H) of authigenic clay minerals has been used extensively in paleoclimate studies. The separation of clay minerals from sediments/soils, using various chemicals, is a prerequisite for isotope ratio measurements, where carbonate, Fe-(oxyhydr)oxides, and organic matter are removed successively from the sediments for a greater clay yield. The commonly adopted organic matter-removal method using hydrogen peroxide (H2O2) is thought to either alter directly the pristine δ2H values of the smectite clay minerals or to introduce organic hydrogen-bearing impurities through the ineffective removal of organic matter. The objective of the present study was to test whether H2O2 treatment can alter the δ2H values of kaolinite (Kln) by comparing two organic matter-removal methods, namely, H2O2 and disodium peroxodisulfate (Na2S2O8) combined with a neutral buffer. In doing so, kaolinite-rich, old (~56 Ma) sediment samples and pure kaolinite internal laboratory reference materials were used to understand the effectiveness and suitability of the above-mentioned methods in clay-sample preparation for δ2H measurements. The δ2H values of the H2O2-treated aliquots show smaller δ2H values than those for the Na2S2O8-treated aliquots. Estimated ambient water δ18O values (−4‰) from the Na2S2O8-treated aliquots agreed well with the bio-phosphate (fish vertebrae) based environmental water δ18O estimation (−3.3‰). The present study indicated, therefore, that δ2H values obtained after Na2S2O8 treatment are likely to be more realistic for paleoclimate reconstruction.