Here, we report the draft, nearly complete genome sequence of the human oral actinobacterium Schaalia odontolytica strain ORNL0103, which was isolated in association with "Candidatus Saccharibacteria" HMT352 strain ORNL0105. The genome was sequenced using a combination of Pacific Biosciences and Illumina platforms and encodes 1,948 proteins and 60 RNAs.