To modify a diene-based rubber whereby the dispersibility of silica and the abrasion resistance or heat buildup resistance are improved.A modified diene-based rubber obtained by adding and reacting, to a diene-based rubber (A), a compound (B) having, in the molecule thereof, a nitroxide free radical stable at an ordinary temperature and in the presence of oxygen, a radical initiator (C) and a radical polymerizable monomer (D) having a functional group in the molecule thereof and a rubber composition and pneumatic tire containing the same.