In this study, the influence of the dietary incorporation of Echinacea purpurea (EP) extract and/or vitamin C on the intestinal histomorphology and some immunological indices were tested in the Nile tilapia (Oreochromis niloticus Linn.). O. niloticus were randomly divided into four groups. The control group G1 was fed on a basal diet, while the G2 and G3 were fed on basal diets, supplemented with EP extract and vitamin C at the doses of 500 mg kg−1 and 400 mg kg−1, respectively. Meanwhile, G4 was fed on a basal diet, supplemented with a mixture of EP extract and vitamin C. After 28 days of feeding, the intestinal tissues were collected for histological observation and immune status, was based on an assay for measuring the phagocytic activity. Furthermore, the expression of the transforming growth factor-beta 1 (TGF-β1), interleukin-1beta (IL-1β), and tumor necrosis factor alpha (TNF-α) genes was evaluated in intestine and head kidney. The results revealed that the G4 successfully surpassed the other groups in terms of the heights of intestinal villi, the number of goblet cells and intraepithelial lymphocytes (IELs), and the phagocytic activity, followed by the G3 and G2. The expression of the IL-1β and TNF-α genes were up regulated only in G4 but in the G3 only the expression of the IL-1β gene was up regulated. Hence, EP extract along with vitamin C could be used as a feed additive in order to improve the structure of the intestinal mucosal epithelium and immune response in tilapia.