Previous experimental observations motivate clarification of configuration stabilities and kinetic processes for intercalation of guest atoms into a layered van der Waals material such as a graphene-SiC system. From our first-principles density functional theory (DFT) calculations, we analyze Dy adsorption and intercalation for graphene on a 6H-SiC(0001) surface, where the system includes two single-atom-thick graphene layers: the top-layer graphene (TLG) and the underling buffer-layer graphene (BLG) above the terminal Si layer. Our chemical potential analysis shows that intercalation of a single Dy atom into the gallery between TLG and BLG is more favorable than adsorption on TLG but that intercalation into the gallery underneath BLG is highly unfavorable. We obtain diffusion barriers of ∼0.45 and 0.54 eV for a Dy atom diffusing on and under TLG, respectively. We find that the direct penetration of a Dy atom from the graphene top into the gallery under TLG is almost inhibited below a temperature of ∼1400 K due to a large global barrier of at least ∼3.5 eV. Instead, we find that a single Dy atom on TLG can easily intercalate by crossing a TLG step (e.g., a zigzag step presaturated by a Dy chain or a reconstructed zigzag step zz57). We also perform DFT calculations for different Dy coverages to demonstrate how the favorability of Dy intercalation, as well as the corresponding interlayer spacings, depend on the coverage. Consequently, we can provide general insight and guidance for extensively studied systems involving intercalation of foreign atoms into graphene on a SiC substrate.