In animal models, the habenula has been identified as a key structure involved in depression. Thanks to recent technological advancements, a burgeoning body of work has also investigated the habenula in the context of human mood disorders. This scoping review aims to synthesize findings from human studies that pertain to the habenula and its relationship with mood disorders. The review was conducted according to PRISMA guidelines. The literature search was performed with PubMed and yielded 93 articles, of which 50 articles were included in the review. We found that the evidence for baseline habenular hyperactivity in human depression is mixed. As for findings from resting-state functional connectivity (RSFC) studies, they were mainly inconsistent across studies. Moreover, we found no evidence indicating that mood disorders are linked to changes in the volume of the habenula. In order to enhance the replicability of findings, given the small size of the habenula, higher image resolution and larger samples are recommended for future studies.