Theileria annulata (T. annulata) is an important hemoprotozoan that causes high morbidity and mortality. Free amino acid levels, being associated with all organ systems, can provide valuable insights into disease processes. In this study, the role and prognostic significance of the amino acid profile in the pathogenesis of the disease in cattle infected with T. annulata were evaluated. In the study, a total of 46 cattle were used, including 31 T. annulata infected cattle (survivor n = 16, nonsurvivor n = 15) and 15 healthy cattle forming the control group. 1-Methylhistidine, 3-Methylhistidine, alanine, cystathionine, gamma aminobutyric acid, glutamic acid, histidine, leucine, lysine, phenylalanine, taurine, tyrosine, valine, and ethanolamine levels were found to be significantly lower in the control group compared to the survivor and nonsurvivor groups. Arginine, citrulline, glutamine, threonine, and tryptophan levels were found to be significantly higher in the control group compared to the survivor and nonsurvivor groups. In animals infected with T. annulata, it was determined that the risk of death increases 6.56 times when the isoleucine level is ≥ 132.69 µmol/L, 3.62 times when the arginine level is ≤ 111.15 µmol/L, 2.38 times when the tyrosine level is ≥ 127.57 µmol/L, and 1.91 times when the asparagine level is ≤ 26.56 µmol/L. Changes in the levels of 21 amino acids, which could play a role in the pathogenesis of the disease among 31 amino acids, were observed. Among these, it was concluded that high levels of isoleucine and tyrosine, as well as low levels of arginine and asparagine, could be used as prognostic indicators.