We describe the case of a man aged 43 years who presented with a 2-week history of a palpable lump in the right proximal penile shaft. This was preceded by a 6-month history of perineal pain, accompanied by erectile dysfunction. An urgent MRI scan of his penis identified a thrombus within the right crus and corpus of the penis. His thrombophilia screen was normal. The patient was started on oral anticoagulation and a phosphodiesterase inhibitor (PDE-5i) to prevent thrombus progression and maintain erectile function. At 5 months, the patients' symptoms had resolved and an MRI showed a reduction in the thrombus size. MRI is a useful imaging modality to diagnose a thrombus within the corpus cavernosum in patients presenting with a history of penile and perineal pain together with a palpable lump. The non-enhancement of the lesion helps to differentiate this from alternative rare lesions within the penis and perineum.