A novel green aqueous mobile phase modified with room temperature ionic liquids (RTILs) was employed in the absence of volatile organic solvents or ion-pairing reagents to analyze thiamine, a very polar compound, by reverse phase high performance liquid chromatography (RP-HPLC). Due to its strongly hydrophilic nature, thiamine was eluted near the column dead time ($t_0$) using a mobile phase without adding RTILs or ion-pairing reagents, even if a 100% aqueous mobile phase, which has weak elution power under reverse phase conditions, was used. Thus, 1-ethyl-3-methyl-imidazolium hexafluorophosphate ([EMIM][$PF_6$]), which has the strongest chaotropic effect, was selected as a mobile phase additive to improve retention and avoid baseline disturbances at $t_0$. Various mobile phase parameters such as cation moiety, chaotropic anion moiety, pH and concentration of RTILs were optimized to determine thiamine at the proper retention time. Method validation was performed to assess linearity, intra- and inter-day accuracy and precision, recovery and repeatability; all results were found to be satisfactory. The developed method was also compared to the current official United States Pharmacopoeia (USP) and Korean Pharmacopoeia (KP) methods using an organic mobile phase containing an ionpairing reagent by means of evaluating various chromatographic parameters such as the capacity factor, theoretical plate number, peak asymmetry and tailing factor. The results indicated that the proposed method exhibited better efficiency of thiamine analysis than the official methods, and it was successfully applied to quantify thiamine in pharmaceutical preparations.