We describe a 10-year-old severe hemophilia B boy with a stop codon mutation of exon 2 in the factor IX gene who developed high inhibitor of 70 Bethesda units (BU) from 12 months of age after exposure to prothrombin complex concentrate for 14 days. The inhibitor spontaneously disappeared within 3 months. The patient, however, exhibited anaphylactic reaction to the administration of prothrombin complex concentrate and factor IX concentrate at ages 15 and 23 months, respectively. Although recombinant activated factor VII was alternatively given, he suffered from progressive hemophilic arthropathy. At the age of 10 years, the boy underwent desensitization to factor IX concentrate and could tolerate factor IX concentrate of 40 U/kg administered on day 9 of desensitization. Unfortunately, the inhibitor of 16 BU was detected on day 6 and rapidly increased to 180 BU on day 9 of desensitization. Rituximab 375 mg/m2 per week was therefore immediately initiated on day 10 and a total of four doses were given. The inhibitor gradually decreased to 21.5 BU after the fourth dose of rituximab. The daily factor IX concentrate administration of 40 U/kg was continued for 1 month and decreased to three times per week for another month, and then to once to twice per week for the remaining 14 months of desensitization. The patient was able to attend regular school and the most recent inhibitor ranged from 4.4 to 10 BU. No proteinuria or alteration of renal function was found. In conclusion, rituximab is a helpful adjuvant to immune tolerance therapy in a hemophilia B boy with inhibitor and anaphylaxis to factor IX concentrate.