Background <p>Low vitamin D (vitD) levels are consistently associated with an increased risk of depression. However, the biological mechanisms underlying this relationship and potential shared genetic overlap remain elusive.</p> Methods <p>We investigated the genetic overlap and causal relationships between depression (<i>N</i> = 589,356) and vitD levels (<i>N</i> = 417,580) using genome-wide association study (GWAS) summary statistics. We performed genome-wide and local genetic correlation analyses, followed by quantification of polygenic overlap variants. Shared genetic loci were identified and mapped to genes, which were further analyzed through gene expression and lifespan brain expression trajectory analyses. Bidirectional causal relationships were examined using multiple Mendelian randomization approaches.</p> Results <p>We observed significant negative genetic correlations (<i>r</i>_<i>g</i> = -0.079) and identified genetic overlap (<i>N</i> = 410 variants). Genes mapped to the 13 shared loci showed opposing expression patterns. Tissue- and cell-specific functional enrichment analyses revealed significant signals related to brain development, with distinct patterns emerging between fetal development and adulthood. Shared genes (<i>TRMT61A</i>, <i>ITIH4</i>, <i>RASGRP1</i>, <i>CTNND1</i>, <i>HERC1</i>, <i>IP6K1</i>, <i>FURIN ESR1</i>, <i>ZMYND</i> and <i>GRM5</i>) exhibited notable expression variation in the brian throughout the lifespan, aligning with functional enrichment findings.</p> Conclusions <p>Our findings elucidate the shared biological mechanisms underlying the relationship between vitD and depression, suggesting that vitD play an important role in the development of depression through altered early neurodevelopmental processes.</p>