Using molecular dynamics (MD) simulations, the frictional properties of the interface between graphene nanoflake and single crystalline diamond substrate have been investigated. The equilibrium distance between the graphene nanoflake and the diamond substrate has been evaluated at different temperatures. This study considered the effects of temperature and relative sliding angle between graphene and diamond. The equilibrium distance between graphene and the diamond substrate was between 3.34 Å at 0 K and 3.42 Å at 600 K, and it was close to the interlayer distance of graphite which was 3.35 Å. The friction force between graphene nanoflakes and the diamond substrate exhibited periodic stick-slip motion which is similar to the friction force within a graphene–Au interface. The friction coefficient of the graphene–single crystalline diamond interface was between 0.0042 and 0.0244, depending on the sliding direction and the temperature. Generally, the friction coefficient was lowest when a graphene flake was sliding along its armchair direction and the highest when it was sliding along its zigzag direction. The friction coefficient increased by up to 20% when the temperature rose from 300 K to 600 K, hence a contribution from temperature cannot be neglected. The findings in this study validate the super-lubricity between graphene and diamond and will shed light on understanding the mechanical behavior of graphene nanodevices when using single crystalline diamond as the substrate.