The Cy/+ rat has been characterized as a progressive model of chronic kidney disease–mineral bone disorder (CKD‐MBD). We aimed to determine the effect of kidney disease progression on intestinal phosphorus absorption and whole‐body phosphorus balance in this model. A total of 48 Cy/+ (CKD) and 48 normal littermates (NL) rats were studied at two ages:​ 20 weeks and 30 weeks, to model progressive kidney function decline at approximately 50% and 20% of normal kidney function. Sodium‐dependent and sodium‐independent intestinal phosphorus absorption efficiency were measured by the in situ jejunal ligated loop method using 33P radioisotope. Our results show that CKD rats had slightly higher sodium‐dependent phosphorus absorption compared to NL rats, and absorption decreased from 20 to 30 weeks. These results are in contrast to plasma 1,25OH2D, which was lower in CKD rats. Gene expression of the major intestinal phosphorus transporter, NaPi‐2b, was not different between CKD and NL rats in the jejunum but was lower in CKD rats versus NL rats in the duodenum. Jejunal ligated loop phosphorus absorption results are consistent with percent net phosphorus absorption results obtained from metabolic balance:​ higher net percent phosphorus absorption values in CKD rats compared with NL, and lower values in 30‐week‐olds compared with 20‐week‐olds. Phosphorus balance was negative (below zero) in CKD rats, significantly lower in 30‐week‐old rats compared with 20‐week‐old rats, and lower in CKD rats compared with NL rats at both ages. These results demonstrate no reduction in intestinal phosphorus absorption with progression of CKD despite lower 1,25OH2D status when assessed by an in situ ligated loop test, which is in contrast to the majority of in vitro studies, and if confirmed in further studies, could challenge the physiological relevance of in vitro findings.