The objective of this work was to develop a high-performance capillary electrophoresis with amperometric detection (CE-AD) method for the determination of pharmacologically active ingredients in extracts of Valeriana medicinal plants. The method was validated for linearity, repeatability, limits of detection (LODs) and limits of quantification (LOQs), etc. The LODs and LOQs of eight compounds were found to be in the range from 1.0 × 10−8 to 1.2 × 10−7 and 3.3 × 10−8 to 4.0 × 10−7 g/mL, respectively. The proposed method was successfully applied for the analyses and comparison of bioactive components in Valeriana samples after a relatively simple extraction procedure, and the resultant “electrochemical profiles” can intuitively demonstrate the content diversity of each electrochemically active ingredient in Valeriana samples from different places and plant parts. It was found the content of bioactive ingredients may vary by an order of magnitude depending on natural conditions, e.g. soil, climate, humidity etc.