Heart disease is characterized by disrupted sleep rhythmicity and suppressed melatonin levels. Here, the underlying mechanisms were studied. Mouse and human pineal glands showed a marked loss of innervating sympathetic axons in disease. Analysis of the superior cervical ganglia (SCG), where these axons originate, showed an accumulation of macrophages, fibrosis, and loss of pineal-innervating neurons in response to heart disease. Local removal of macrophages in the SCG restored pineal innervation and melatonin secretion, highlighting the means of macrophage-based therapies in heart disease.