Lichen Sclerosus: This condition is characterized by thinning of the skin, which can lead to hyperpigmentation and pain. It is a common cause of genital skin lesions and can affect the base of the penis.

Psoriasis: Genital psoriasis can cause hyperpigmentation and pain due to the inflammatory nature of the disease. The base of the penis is a common area for psoriatic lesions.
Eczema/Dermatitis: Contact dermatitis or atopic dermatitis can cause skin irritation, leading to hyperpigmentation and pain at the base of the penis.
Tinea Cruris (Jock Itch): A fungal infection that can cause itching, redness, and hyperpigmentation in the groin area, including the base of the penis.

Squamous Cell Carcinoma: Although less common, skin cancers like squamous cell carcinoma can present with hyperpigmentation and pain. Early detection is crucial for effective treatment.
Malignant Melanoma: A type of skin cancer that can arise from pigmented lesions. It is critical to rule out melanoma due to its high mortality rate if left untreated.
Syphilis: The secondary stage of syphilis can cause a variety of skin manifestations, including hyperpigmentation, and must be considered due to its potential for serious complications if not treated.

Morphea: A rare condition characterized by localized scleroderma, which can cause skin thickening and hyperpigmentation.
Vitiligo: Although it typically presents with hypopigmentation, in some cases, it can be associated with hyperpigmentation around the edges of the affected areas.
Fixed Drug Eruption: A rare condition caused by an adverse reaction to medication, which can result in hyperpigmentation and pain, typically recurring at the same site each time the offending drug is taken.