Heat stress has a serious impact on nutrient digestion and absorption in broiler chickens. This study aimed to investigate the effects of chronic heat stress (CHS) on the mRNA expression of digestive enzymes and nutrient transporter genes in thermally manipulated (TM) broiler chickens. The evaluated genes encompassed pancreatic lipase, trypsin, amylase, maltase, and alkaline phosphatase as well as certain glucose transporter (GLUT2, SGLT1), amino acid transporter (y+LAT1, CAT1), and fatty acid transporter (FABP1, CD36) genes in the jejunal mucosa. Thermal manipulation was carried out at 39°C and 65% relative humidity for 18 h daily from embryonic days (ED) 10-18, while CHS was induced by raising the temperature to 35°C for 7 D throughout post-hatch days 28 to 35. After 0, 1, 3, 5, and 7 D of CHS, the pancreas and jejunal mucosa were collected from the control and TM groups to evaluate the mRNA expression by relative-quantitative real-time qRT-qPCR. Thermal manipulation significantly decreased the cloacal temperature (Tc) and the hatchling weight, and improved weight gain in broilers during post-hatch life and CHS. In addition, TM decreased the mortality rate during CHS. During CHS, the mRNA expression levels of SGLT1, GLUT2, FABP1, and trypsin were significantly decreased after 1 D in control chickens, and this lower expression persisted until day 7, after which it further decreased. In contrast, in TM chickens, SGLT1, GLUT2, and FABP1 expression decreased after 3, 5, and 7 D of CHS, respectively, while no significant change in trypsin expression was observed throughout the CHS period. Moreover, it was found that TM significantly modulated the mRNA expression dynamics of CD36, alkaline phosphatase, y+LAT1, CAT1, lipase, amylase, and maltase during CHS exposure. The findings of this study suggest that, in broiler chickens, TM has a long-lasting impact on nutrient digestion and absorption capabilities as well as Tc, mortality rates, and BW during CHS.