Clostridium perfringens is one of the highest dominant spore-forming foodborne pathogens, which is widely distributed and causes severe diseases in humans and animals. Poultry is the main host of this pathogen. In this study, we investigated the prevalence, antibiotic resistance pattern, and toxin-encoding genes of C. perfringens isolated from chicken with necrotic enteritis. Twelve of C. perfringens strains were isolated from 100 intestinal samples (native and Hubbard chickens) with a percentage of 12% and subsequently confirmed by PCR; all strains carried alpha-toxin gene and were negative for other major toxin genes (Beta, Epsilon and Iota). The C. perfringens isolates showed highly resistance (100%) to most of the antibiotics tested; Ampicillin, Amoxicillin, Amoxicillin-clavulanic acid, Erythromycin, Lincomycin, Metronidazole, Neomycin, Oxytetracycline, Penicillin, Spectinomycin, Streptomycin, but showed sensitivity with a low percentage (25% or low) for Colistin sulphate, Doxycyclin, Enrofloxacin, Norfloxacin and Sulfamethoxazole-trimethoprim. However, virulence genes were detected with a different percentage of 100%, 75% and 16.7 with Cpe, netB and Tpel respectively. In the examination of antimicrobial-resistant genes the examined isolates showed 100%, 75% and 25% with (tetK) tetracyclines, (Bla) B. lactamase resistant gene and macrolide (ermB) respectively. Our findings confirmed that the diseased cases with different sings of multidrug-resistant C. perfringens strains could be regarded as one of the concerning pathogens in broiler chickens and its products. Widespread monitoring of C. perfringens isolates is strongly suggested.