Ian Jackson and Jack Fisher published one of the earliest reports on microsurgical applications for craniofacial patients in 1989. Since that time, applications of craniofacial surgery and microsurgery have significantly expanded and become more refined. However, there remain certain specific clinical problems in cleft and craniofacial surgery in which traditional craniofacial methods provide variable success or suboptimal outcomes. The purpose of the current study is to share our experience using an integrated approach of craniofacial and microsurgical methods to provide optimal surgical solutions to this complex patient population. The authors performed a retrospective review of 17 patients that utilized craniofacial microsurgery in setting of cleft and craniofacial syndromes performed by the senior author from July 2013 to July 2020. 22 free flaps were performed for 17 patients. The patient age at time of flap reconstruction ranged from 10 to 48 years (mean 21.4 years). There were 8 females and 9 males. There was one total flap loss. Based on our collective experience, the authors present a comprehensive algorithm for the role of microsurgical reconstruction in cleft and craniofacial patients. There are several situations in craniofacial surgery which traditional reconstructive methods require numerous operative interventions to achieve suitable outcomes. Craniofacial Microsurgery techniques can bring in new tissue and may prevent the need to manipulate scarred and multiply operated tissues. The craniofacial surgery team should not hesitate to apply microsurgical solutions to these situations for optimal results.