Patients presenting with coarctation of the aorta (CoA) may also suffer from co-existing transverse arch hypoplasia (TAH). Depending on the risks associated with the surgery and the severity of TAH, clinicians may decide to repair only CoA, and monitor the TAH to see if it improves as the patient grows. While acutely successful, eventually hemodynamics may become suboptimal if TAH is left untreated. The objective of this work aims to develop a patient-specific surgical planning framework for predicting and assessing postoperative outcomes of simple CoA repair and comprehensive repair of CoA and TAH. The surgical planning framework consisted of virtual clamp placement, stenosis resection, and design and optimization of patient-specific aortic grafts that involved geometrical modeling of the graft and computational fluid dynamics (CFD) simulation for evaluating various surgical plans. Time-dependent CFD simulations were performed using Windkessel boundary conditions at the outlets that were obtained from patient-specific non-invasive pressure and flow data to predict hemodynamics before and after the virtual repairs. We applied the proposed framework to investigate optimal repairs for six patients (n = 6) diagnosed with both CoA and TAH. Design optimization was performed by creating a combination of a tubular graft and a waterslide patch to reconstruct the aortic arch. The surfaces of the designed graft were parameterized to optimize the shape. Peak systolic pressure drop (PSPD) and time-averaged wall shear stress (TAWSS) were used as performance metrics to evaluate surgical outcomes of various graft designs and implantation. The average PSPD improvements were 28% and 44% after the isolated CoA repair and comprehensive repair, respectively. Maximum values of TAWSS were decreased by 60% after CoA repair and further improved by 22% after the comprehensive repair. The oscillatory shear index was calculated and the values were confirmed to be in the normal range after the repairs. The results showed that the comprehensive repair outperforms the simple CoA repair and may be more advantageous in the long term in some patients. We demonstrated that the surgical planning and patient-specific flow simulations could potentially affect the selection and outcomes of aorta repairs.