Avian coccidiosis is a widespread and economically significant disease in poultry. At present, treatment of coccidiosis mainly relies on drugs. Anticoccidial drugs can be divided into two categories: ionophorous compounds and synthetic drugs. However, the emergence of drug-resistant strains has become a challenge for coccidiosis control with anticoccidial drugs. To gain insights into the molecular mechanism governing the drug resistance of Eimeria tenella, two drug-resistant strains of E. tenella, one maduramicin-resistant (MRR) strain and one diclazuril-resistant (DZR) strain, were generated. We carried out comparative transcriptome analyses of a drug-sensitive strain (DS) and two drug-resistant MRR and DZR strains of E. tenella using RNA-sequencing. A total of 1,070 differentially expressed genes (DEGs), 672 upregulated and 398 downregulated, were identified in MRR vs. DS, and 379 DEGs, 330 upregulated and 49 downregulated, were detected in DZR vs. DS. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed to better understand the functions of these DEGs. In the comparison of DZR vs. DS, some DEGs were involved in peroxisome, biosynthesis of unsaturated fatty acids, and fatty acid metabolism. In the comparison of MRR vs. DS, some DEGs were involved in glycolysis/gluconeogenesis, regulation of actin cytoskeleton, and DNA replication. In addition, some DEGs coded for surface antigens that were downregulated in two drug-resistant strains involved invasion, pathogenesis, and host-parasite interactions. These results provided suggestions for further research toward unraveling the molecular mechanisms of drug resistance in Eimeria species and contribute to developing rapid molecular methods to detect resistance to these drugs in Eimeria species in poultry.