Microwave-assisted Fmoc solid phase peptide synthesis (SPPS) was applied in combination with the isopeptide strategy to establish a new method for the rapid synthesis of difficult sequence-containing peptide. A model peptide (8Q_Ser) was produced in one day using the method developed, in contrast with two weeks using the isopeptide method. Both methods produced the desired peptide in high yield and purity, while classical SPPS did not result in the desired product.