Clean any dead leaves, water or other material away from the flashing. The flashing is the bendable metal sheets -- often made of aluminum, copper, lead or galvanized steel -- that come from beneath the shingles and lap up over the edge of the skylight's frame.
Peel back the shingles around the skylight to expose all of the outside edges of the pieces of flashing. Pull the shingles back far enough to give yourself room to apply flashing cement to the edges of the flashing that lie farthest back beneath the shingles.
Spread flashing cement with a putty knife to create a seal along the joints where the flashing meets the roof underneath the shingles. Also seal the joints between the sections of flashing. Apply the cement to the flashing on all sides of the skylight.