Climb onto the roof using a ladder. Inspect the metal flashing around the skylight for any signs of damage or corrosion. Run water over any suspected leak areas using a hose and have someone inside the house watch for leaks.
Pull out the nails holding the flashing in place and pry up any other objects covering the flashing using a small pry bar. If the flashing is damaged or corroding, install a replacement.
Drive screws through the flashing’s nail holes--screws will not pop out and lead to leaks in the future. Spread a thick bead of silicone caulk to both sides of the flashing’s edges.
Climb into your house’s attic and locate the skylight shaft. Wrap insulation around the shaft if you do not see any present, driving nails into the studs to hold the insulation in place.