Climb on the roof, safely, using a ladder. Thoroughly inspect the roof for any scratches and holes along the seams and entirety of the roof.
Remove the old sealant using a utility and putty knife once you find the leak.
Wash the area where the leak was with a non-petroleum or non-citrus-based soap and water. Dry the area off with rags.
Fill in the area of the leak with new sealant using a caulking gun. This sealant needs to be non-petroleum-based and be flexible when it dries.
Spread the new sealant smooth over the area of the leak. Make sure that you fill in all the gaps and holes, leaving a little extra so there is room for shrinkage. Also make sure the sealant is still good around all holes on the roof such as fasteners and screws.