The purpose of the present invention is to provide a modified polymer that significantly reduces heat build-up due to the modification when the modified polymer is formed into a rubber composition, a rubber composition containing the modified polymer, and a pneumatic tire in which the rubber composition is used. The modified polymer of the present invention is a modified polymer obtained by modifying a styrene-conjugated diene copolymer (A) with a nitrone compound (B). In the modified polymer, the content of styrene units in the styrene-conjugated diene copolymer (A) is 10% by mass or greater, and the proportion of vinyl bonds among all the double bonds contained in the styrene-conjugated diene copolymer (A) is 5 mol % or greater.