Giant condyloma acuminatum occurs infrequently in children and adolescents. It is a challenging condition which is difficult to treat with both surgical and medical modalities. We present a case of a 15-year-old boy with giant condyloma acuminatum of the glans penis refractory to several therapeutic modalities. The lesions were treated successfully with a novel combination of Mycobacterium indicus pranii immunotherapy and acitretin. There was no recurrence of lesions after two years of follow-up.