Nigella sativa seed contains a bioactive compound known as thymoquinone (TQ) which is prominent for its pharmacological properties such as antioxidant; anti-microbial, antibacterial and anti-inflammatory hence, becomes an important ingredient in Herbal Medicinal Products (HMPs). However, adulteration of HMPs has raised concerns among consumers. This study aims to extract and characterize TQ from Nigella sativa based products. TQ was isolated from raw Nigella sativa seeds using methanolic and aqueous extraction methods. Extracts were subject to qualitative and quantitative analysis using High-Performance Liquid Chromatography (HPLC). Both extraction methods produced TQ extracts with methanol extraction yielded 63.4 µg/mL while aqueous extraction method produced 15.3 µg/mL. Quantitative analysis of 13 commercialized products containing Nigella sativa such as oil, capsule, facial foam, shower foam, and toothpaste showed presence of TQ at varying concentration. The effectiveness of TQ exhibits its pharmacological activity is questionable because the concentration of TQ in the product was not stated on the packaging.