The objective of this study was to determine the effect of phytase supplementation and coccidial vaccine challenge (CVC) on jejunal and ileal nutrient and energy digestibility and the expression of genes of some markers of inflammation and nutrient transporters in broilers. Ross 708 broilers (384 males) were randomly assigned to six treatments in a factorial arrangement with two levels of CVC (0× or 25×) and three levels of phytase [0, 1000, or 5000 phytase units (FTU) kg^-1 diet] with eight birds per pen and eight replicates per treatment. On day 42 post hatching, 192 birds received no challenge (NCH) or challenged (CHA) with 25× coccidial vaccine. Birds received the experimental diets from day 49 post hatching until day 55. Jejunal dry matter and energy digestibility decreased (P < 0.05) with CVC, but phytase supplementation increased (P < 0.05) nitrogen (49.1%–55.2%) and phosphorus (18.0%–58.3%) digestibility. Ileal nitrogen and P digestibility increased (P < 0.05) with phytase supplementation. In the jejunum, CVC (P = 0.053) and phytase (P = 0.063) showed a tendency to decrease the expression of active sodium-dependent phosphate transporter. The results from this study show that the interaction between CVC and phytase resulted in higher feed efficiency (at the level of 5000 FTU), lower jejunal dry matter digestibility (DMD), and digestible energy (at the level of 1000 FTU). Also, older broilers, especially those with gastrointestinal tract inflammation (CHA), may benefit more from phytase super dosing compared with the NCH birds.