The purpose of the present study was to investigate the dynamic changes of MHC-DQB1 mRNA expression in sheep infected with Echinococosus granuclosus. A total of 14 healthy Chinese merino sheep were experimentally infected with E. granuclosus. The blood samples were collected on days 0 (initiation of the infection), 7, 21, 30, and 60 post-infection, respectively. On day 60 post-infection, when the experiment was terminated, all sheep were euthanized to make a diagnosis of cystic echinococcosis (CE) using routine meat inspection and microscopical examination, respectively. The sheep were then divided into two groups according to the diagnostic results: group A (n = 8) consisted of sheep which were diagnosed as CE infection, while group B (n = 6) comprised sheep diagnosed as self-cured or healthy controls. Blood samples obtained during the period of the study were correspondingly divided into groups A and B. The mRNA expression levels of DQB1 revealed significant alterations detected at different stages of E. granuclosus infection in the two groups. Results showed that in group A, DQB1 mRNA expression underwent a progressive increase from day 0 to day 21 post-infection (P = 0.073), and suddenly, suffered from a dramatic drop until day 30 post-infection, and then jumped rapidly and peaked on day 60 post-infection (P = 0.004). Meanwhile, in group B, DQB1 mRNA expression displayed a sharp increase from day 0 to day 7 post-infection (P = 0.000), which thereafter showed a marked decrease until day 30 post-infection, and experienced a plateau from day 30 to day 60 post-infection, remaining at or above that on day 0. It is concluded that DQB1 mRNA expression levels varied in different stages of E. granuclosus infection in sheep. In addition, it appears that the ability to eliminate the parasites possibly depends, at least in part, on the DQB1 expression in the early stage of infection, especially in the first week post-infection.