In contrast to the wide applications of recombinant bifunctional fusion proteins in clinical usage, the systematic study for the pharmacokinetics (PK) of bifunctional fusion proteins is left blank. In this report, recombinant fusion proteins consisting of transferrin (Tf) and growth hormone (GH) or granulocyte colony-stimulating factor (G-CSF) have been constructed as a model for studying the PK of bifunctional fusion proteins. The results showed that the insertion of different linkers between the two protein domains altered the binding affinities of the fusion proteins to both domain receptors, and that the fusion proteins' plasma half-lives were greatly affected. A strong correlation between GH receptor binding affinity and plasma half-life of GH-Tf fusion proteins was observed. In addition, we demonstrated that the intracellular processing after receptor binding plays an important role in determining the half-life of fusion proteins. While the binding of the GH domain to the GH receptor will lead to endocytosis and lysosomal degradation in target cells, binding of the Tf domain to the Tf receptor may recycle the fusion protein and prolong its plasma half-life. To further confirm the effects of receptor binding on plasma half-life, G-CSF-Tf bifunctional fusion proteins with the same three linkers as GH-Tf were evaluated. While the 3 fusion proteins showed a similar G-CSF receptor binding affinity, the G-CSF-Tf fusion protein with the higher Tf receptor binding affinity exhibited longer plasma half-life. The linker insertion further demonstrated the involvement of Tf in recycling and prolonging plasma half-life. Based on our results, a model was developed to summarize the factors in determining the PK of bifunctional fusion proteins. Our findings are useful for predicting the plasma half-lives, as well as for improving the pharmacokinetic profiles of therapeutic bifunctional fusion proteins by applying linker technology.