Clostridium perfringens is the causative agent of necrotic enteritis leading to significant losses in the poultry industry. Dichloromethane and n-hexane extracts of aerial parts of Artemisia annua (Asteraceae) exhibited activity against C. perfringens with minimum inhibitory concentrations (MIC) of 185 and 270 μg/mL, respectively. Bioassay-guided fractionation of the extracts gave several active fractions (MIC between 75 and 600 μg/mL). Investigations of the most active fractions resulted in the isolation and characterization of the polyacetylene ponticaepoxide (MIC between 100 and 200 μg/mL) and (+)-threo-(5E)-trideca-1,5-dien-7,9,11-triyne-3,4-diol (MIC between 400 and 800 μg/mL), the flavonols chrysosplenol D (MIC between 200 and 400 μg/mL) and casticin (slight inhibition at 800 μg/mL), and 2,4-dihydroxy-6-methoxyacetophenone (slight inhibition at 800 μg/mL). Also, the coumarin scopoletin and the sesquiterpene lactone artemisinin were isolated from active fractions but showed no inhibition of C. perfringens growth at 800 and 2000 μg/mL, respectively. Fractions containing essential oil components with camphor constituting >60% did not show inhibition of C. perfringens up to 1600 μg/mL. Extracts and some active fractions showed higher antibacterial effect than individual bioactive compounds, suggesting that synergistic effects may underlie the observed antibacterial effect. The present study adds new valuable information on the antibacterial effect of A. annua against C. perfringens.