Feeding timing has recently been recognized as important for cardiometabolic health. However, it remains unknown how abnormal feeding timing influences lipid metabolism, which may be relevant to cardiovascular disease risk. Here, we investigated how breakfast skipping (BS) combined with a Western diet (WD), which is a typical unhealthy feeding behavior combination in humans, affects lipid metabolism in rats. Wistar male rats were fed a WD (sucrose 52%, casein 20%, lard 15%, corn oil 2%, and cholesterol 1%) during zeitgeber time (ZT) 12-0 in the control group and ZT16-4 in the BS group. This experiment was conducted for 14 days. The BS rats showed massive rhythmic hyper-remnant-like particle (RLP)-cholesterolemia. Circadian oscillations of almost clock genes and cholesterol synthesis-related sterol regulatory element-binding protein 2 and 3-hydroxy-3-methylglutaryl-CoA synthase was delayed due to BS. The average mRNA level of cholesterol degradation-related genes, including sterol 12 α-hydroxylase and ATP binding cassette subfamily G member 5, was decreased in response to BS. In adipose tissue, circadian oscillation of clock genes was also delayed by BS, and the average mRNA level of adipose triglyceride lipase and lipoprotein lipase was enhanced. These data suggest that the combination of BS and WD is associated with massive rhythmic hypercholesterolemia, which may involve altered circadian oscillation of hepatic and adipose clock genes and changes in lipid metabolism. Although lipid metabolism differs between rodents and humans, particularly in lipoprotein profiles, these findings may provide insight into mechanisms linking feeding timing and altered lipid metabolism.