Chicken coccidiosis caused by Eimeria species leads to tremendous economic losses to the avian industry worldwide. Identification of parasite life cycle specific antigens is a critical step in recombinant protein vaccine development against Eimeria infections. In the present study, we amplified and cloned the microneme-2 (EtMIC2) gene from Eimeria tenella wild type strain SD-01, and expressed the EtMic2 protein using Pichia pastoris and Escherichia coli expression systems, respectively. The EtMic2 proteins expressed by P. pastoris and E. coli were used as vaccines to immunize chickens and their protective efficacies were compared and evaluated. The results indicated that both P. pastoris and E. coli expressed EtMic2 proteins exhibited good immunogenicity in stimulating host immune responses and the Pichia expressed EtMic2 provided better protection than the E. coli expressed EtMic2 did by significantly increasing growth rate, inducing high specific antibody response, reducing the oocyst output and cecal lesions. Particularly, the Pichia expressed EtMic2 protein exhibited much better ability in inducing cell mediated immune response than the E. coli expressed EtMic2.