The present study aimed to evaluate the accuracy of digitally designed surgical splints generated with milling technology (material subtractive procedure) and with 3D printing technology (material additive procedure) through a customized approach in the planning of surgical orthognathic splints. Cone beam computed tomography (CBCT) examinations and scanned dental models of 10 subjects who had required surgical treatment of skeletal malocclusion were included. Simulation of the orthognathic surgery was performed according to dento-skeletal and aesthetic characteristics of the subjects and the visual treatment objective (VTO), using Dolphin3D software (Dolphin Imaging, version 11.0, Chatsworth, CA, USA). Afterward, the Appliance Designer software (3Shape A/S, Copenhagen, Denmark) was used to digitally design the surgical splints that were generated twice using laser stereolithography technology (DWS 0.29D, DWS, Vicenza, Italy) and milling technology (Sirona inLab MC X5). Finally, each physical splint was digitalized using a desktop scanner (D500 3D, 3Shape A/S, Copenhagen, Denmark) in order to perform deviation analysis using the original project as a reference. The relative percentage of matching (trueness) was calculated (Geomagic Control X software (3D Systems, version 2018.1.1, 3D Systems, Rock Hill, SC, USA). An Independent Student’s t-test was used to statistically analyze the data. The milled splints showed a lower value of root to mean square (RMS) relative to the original project (0.20 mm ± 0.018) compared to the prototyped splints (0.31 ± 0.021) (p < 0.001). According to the present findings, surgical splints generated with milling technology present higher trueness compared with 3D printing technology.