Functional and esthetic final reconstruction of the cleft maxilla is still challenging. Current reconstructive and augmentation techniques do not provide sufficient bone and soft tissue support for the predictable rehabilitation with dental implants due to presence of maxillary bone critical size defects and soft tissue deficiency, scaring and poor vascularity. In this article the protocol for the use of 3D virtual surgical planning and microvascular tissue transfers for the reconstruction and rehabilitation of cleft maxilla is presented. Twenty-five patients (8 male/17 female) aged 14–41 years old with cleft-associated critical size defects were treated by 3D-virtual planned microvascular tissue transfers taken either from fibula, iliac crest, radial forearm, or medial femoral condyle. Follow-up lasted 1–5 years. No significant bone resorption (p > 0.005) nor volume loss of the graft was observed (p = 0.645). Patients received final permanent prosthetic reconstruction of the anterior maxilla based on 2–5 dental implants, depending on the defect severity. This is the first study presenting the use of virtual planning in the final restoration of the cleft maxilla with microvascular tissue transfers and dental implants. Presented protocol provide highly functional and aesthetic results.