A series of hydrophilic ionic liquids (ILs) were investigated as extractants for the quantitative determination of valerenic and acetoxyvalerenic acids in Valerianae radix. The influence of different factors, e.g. type of cation and anion, alkyl chain length, concentration, temperature, extraction time and solid-liquid ratio, was investigated. The results obtained showed that the extraction yield is strongly dependent on the cation type. The best outcome was obtained with IL capable of forming micelles in aqueous solution, e.g. 1-decyl-3-methylimidazolium chloride. As a result, an alternative protocol for the quantification of sesquiterpenic acids in valerian was developed and validated.