Discolored penis head. The condition tends to develop on the penis. It must be diagnosed by a doctor through a physical exam. Sign in to make a comment Sign in to your personal account. Thank Doctor Thank. The discoloration on the penis will fade in time; however, if he feels pain or discomfort, medical attention should be sought. The penis may turn reddish, or flat brown patches may form. An urologist's nightmare! Determining the cause will enable the doctor to prescribe the correct treatment.