RNA processing is necessary for the protozoan parasite Toxoplasma gondii to accomplish differential gene expression required during life cycle stage transitions. Here, we show how RNA capping, the first major pre-mRNA processing event, safeguards transcriptome integrity in Toxoplasma. A functional RNA capping system of Toxoplasma consists of separate RNA triphosphatase (TgRT), guanylyltransferase (TgGT), and guanine-N7-methyltransferase (TgGMT) enzymes, which together add 5" 7-methylguanosine (m7G) cap to RNA. In vitro, these capped RNAs bind to the Toxoplasma translation initiator factor, eIF4E, and are translated to protein upon transfection in the parasite. Biochemical and genetic characterization reveal that among three capping enzymes, triphosphatase (TgRT) is unique and a member of the tunnel family of metal-dependent phosphohydrolases, structurally and mechanistically unrelated to the human cysteine-phosphatase-type RNA triphosphatases. Using cap sequencing, we demonstrate that the knockdown of TgRT diminished global m7G-capped transcripts of genes primarily related to DNA packaging and cell membranes, which resulted in a complete arrest of parasite replication in culture and in vivo protected mice from lethal infection. Overall, this study shows the critical role of TgRT in gene expression and Toxoplasma survival, which may be conserved in the related parasites, thereby presenting RNA triphosphatase as an attractive target for protozoan infections.