Background The radial forearm osteocutaneous free flap is considered to be the standard technique for penile construction. One year after their operation, most patients experience a softened phallus, so that they suffer from difficulties in sexual intercourse. In this report, we present our experience with phalloplasty by radial forearm osteocutaneous free flap, as well as an evaluation of the etiology and treatment of the softened phallus. Methods Between March 2005 and February 2010, 58 patients underwent phalloplasty by radial forearm osteocutaneous free flap. Most of their neophallus had been softened subjectively and among them, 12 patients who wanted correction were investigated. We performed repetitive fat injection, artificial dermis grafting, silicone rod insertion, and rib bone with cartilaginous tip graft. Physical examination, plain radiograph, computed tomography, bone scintigraphy, and satisfaction scores were investigated. Results Most of the participants' penises have been softened after phalloplasty, and the skin elasticity had been also decreased. On plain radiograph, the distal end of the bone was self-rounded; however, the bone shape of the neophallus had no significant interval changes or resorption. Computed tomography showed equivocal density of cortical bone. On bone scintigraphy, the bone metabolism was active at 3 months postoperatively, and remained active 9 years postoperatively. Conclusions The use of a rib bone with cartilaginous tip graft could be an option for improvement of the softened phallus. Silicon rod insertion is also worth considering for rigidity of the softened phallus. Decreased rigidity due to soft tissue atrophy could be alleviated with repeated fat injection and artificial dermis grafting.