For thousands of years, leaves from the Ginkgo biloba tree have been a common treatment in Chinese medicine. The present study was conducted to investigate the effects of dietary ginkgo biloba leaf extract (GBE) supplementation on growth performance, plasma biochemical parameters, fish composition, immune responses, liver histology, and immune and apoptosis-related genes expression of hybrid grouper (Epinephelus lanceolatus♂ × Epinephelus fuscoguttatus♀) fed high lipid diets. A basal diet supplemented with GBE at 0, 0.50, 1.00, 2.00, 4.00 and 10.00 g kg−1 was fed to hybrid grouper for 8 weeks. The study indicated that dietary GBE did not improve growth performance and feed utilization but it reduced intraperitoneal fat rate. There were no significant differences in condition factor, viscerosomatic index, hepatosomatic index, spleen index, relative gut length, food intake, protein deposit rate and survival among all groups (P > 0.05). Dietary supplementation with 0.50–4.00 g GBE kg−1 diets effectively increased plasma HDL content and decreased plasma GLU, LDL and TG content in fish. Furthermore, dietary GBE had a significant effect on moisture, crude protein and lipid in the liver, and protein in the whole body of fish (P < 0.05). Dietary supplementation with 0.50–1.00 g GBE kg−1 diets effectively decreased occurrence rates of the hepatocyte swelling, hepatocyte vacuolization, and nuclei shifting to the cellular periphery cytoplasmic vacuolization, meanwhile hepatic antioxidant enzymes (SOD, CAT and T-AOC) activities significantly increased whereas MDA content significantly decreased in fish fed diets supplemented with GBE (P < 0.05). Moreover, dietary GBE up-regulated the expression of antioxidant genes (CAT, GPx and GR), immune-related genes (MHC2 and TLR3) and anti-inflammatory cytokines (IL-10 and TGF-β1), while dietary supplementation with 0.50–4.00 g GBE kg−1 diets down-regulated apoptosis-related genes (p53, caspase-9, caspase-8 and caspase-3) expression in the head kidney of hybrid grouper. These results indicated that hybrid grouper fed diets supplemented with GBE did not improve growth performance and feed utilization but it had hypolipidemic effects, improved hepatic antioxidant status, maintained normal liver histology and preserved liver function, increased immune-related genes expression and decreased apoptosis-related genes expression in the head kidney of hybrid grouper.