The feline leukemia virus (FeLV) is a complex disease that affects mainly the immune and hematological systems of cats. And because the thymus was closely associated with the immune system, the aim of this study was to quantify the morphological changes in the thymus of naturally infected and uninfected animals. Thymus morphological changes were evaluated by quantifying the following parameters: thymocytes, fat tissue, thymic corpuscles, connective tissue, and type I and III collagen. This study analyzed a total of seven cats, five in the negative group (Fn) and two in the positive (Fp) group. The areas occupied by thymocytes in FeLV negative (Fn) and positive (Fp) animals were, respectively, 55.16% ± 6.15% and 44.81% ± 6.15% (p = 0.39); adipocytes, 42.14% ± 5.97% (Fn) and 53.42% ± 11.3% (Fp) (p = 0.34); blood vessels, 0.85% ± 0.24% (Fn) and 1.75% ± 0.52% (Fp) (p = 0.15). Whereas thymic corpuscles occupied an area of 0.68% ± 0.19% in negative animals (Fn) only. The connective tissue covered area varied between 12.05% ± 0.68% (Fn) and 10.34% ± 0.62% (Fp) (p = 0.009). Collagen type I (p = 0.30) and type III (p = 0.59) were present in, respectively, 1.73% ± 0.3% and 0.44% ± 0.09% in Fn, and 1.44% ± 0.36 and 0.44% ± 0.13% in Fp. The FeLV virus was not able to completely modify the thymus structure of infected animals, considering the areas occupied by thymocytes, adipose tissue, blood vessels and also type I and III collagens. However, the connective tissue underwent a certain degree of remodeling since less connective tissue area was observed in FeLV infected animals. The absence of thymic corpuscles in immunosuppressed animals suggests a possible connection to thymopoiesis.