Meat and bone meal (MBM) is a high-quality alternative protein source used to replace fishmeal (FM). However, the molecular mechanisms of over-substituted FM by MBM resulted in growth reduction are still not clear. The objective of the study was to evaluate the effect of FM replacement by MBM on the concentration of postprandial free amino acid (FAA) and mRNA abundance of peptide and amino acid transporters in juvenile turbot (Scophthalmus maximus L.). Fish were fed with FM diet (60% FM), MBM diet (33% FM + 34.2% MBM) and MBM + AA diet (MBM diet with essential amino acid (EAA) added to match the AA profile of FM) for 30 days. Results showed that compared with the FM diet, MBM diet led to a reduction in FAA concentration peak values in plasma and muscle. MBM + AA diet significantly elevated the peak values of FAA concentrations to FM diet level in plasma, but not in muscle. Furthermore, compared with FM diet, MBM diet significantly increased gene expression of PepT1 and major amino acid transporters in intestine, whereas MBM diet greatly downregulated gene expression of T-type amino acid transporter-1, system ASC amino acid transporter-2 and cationic amino acid transporter-2 in muscle. Supplemented EAA did not ameliorate these different effects in intestine and muscle. Overall, this study provided a comprehensive explanation for the relationship between diet, FAA concentrations and AA transportations, which provides a molecular basis for further using MBM to replace FM in aquafeeds.