The virtual approach in physical and forensic anthropology is increasingly used to further analyze human remains, but also to propose new didactic means for visualization and dissemination of scientific results. Computerized facial approximation (FA) offers an alternative to manual methods, but usually requires a complete facial skeleton to allow for the estimation of the facial appearance of an individual. This paper presents the case of Tycho Brahe, Danish astronomer born during the XVIth century, whose remains were reanalyzed at the occasion of a short exhumation in 2010. Cranial remains of Brahe were poorly preserved, with only a partial facial skeleton, and virtual anthropology tools were used to estimate the missing parts of his skull. This 3D restoration was followed by a FA using TIVMI-AFA3D, subsequently textured with graphic tools. The result provided an interesting estimate that was compared with portraits of the astronomer. The impact of the missing data estimation was investigated by performing FAs on 10 complete test subjects and the same 10 subjects after cropping and estimating 50% of the landmarks (reproducing the preservation state of Tycho Brahe’s cranial remains). The comparison between the FA based on the complete and incomplete skulls of the same subject produced a visual assessment of the estimation impact on FAs which is relatively low. This procedure is an alternative to manual methods and offers a reproducible estimate of a face based on incomplete cranial remains. Although the case report concerns a historical individual, the robust automatic estimation of missing landmarks followed by a FA has value for forensic caseworks as a support to the identification process.