β-Guanidinopropionic acid (β-GPA) feeding inhibits growth-associated gain of body mass. It remains unknown, however, whether and how β-GPA feeding affects growth-associated increase in white adipose tissue (WAT) mass. We examined the effects of 4- and 8-week β-GPA feeding on serum myostatin levels and expression of genes and proteins related to adipogenesis, lipolysis, and liposynthesis in epididymal WAT (eWAT) and brown adipose tissue (BAT) in 3-week-old, juvenile male mice. Body, eWAT, and muscle weights were significantly lower in β-GPA-fed mice than in controls after feeding. Four- but not 8-week-β-GPA feeding increased the serum myostatin level. Incubation of C2C12 myotubes with β-GPA (1 mM) significantly promoted myostatin mRNA expression. The protein expression of peroxisome proliferator-activated receptor gamma coactivator 1 α (PGC-1α) and peroxisome proliferator-activated receptor α (PPARα) was up-regulated in GPAF eWAT at week 4, but down-regulated at week 8. There was no significant difference in the protein expression of adipocyte triglyceride lipase (ATGL), hormone-sensitive lipase (HSL), fatty acid synthase (FAS), and acetyl-CoA carboxylase (ACC) between groups in eWAT. In BAT, no significant difference was found in the protein expression of PGC-1α, PPARα, ATGL, and HSL between β-GPA-fed and control mice, whereas that of FAS and ACC was significantly lower in β-GPA-fed mice at week 8. Uncoupling protein 1 was expressed higher in β-GPA-fed mice both at weeks 4 and 8 than that in controls. Thus, the mechanism by which β-GPA feeding in early juvenile mice inhibits growth-associated increase in eWAT mass may differ between early and later periods of growth.