Scrape the window sill with a putty knife to remove any flaking or peeling paint. Sand the wood grain fibers using a 120-grit sanding block. Dust off the sill with a dust brush. Vacuum the dust and debris out of the cracks.
Fill the cracks with a wood putty filler. Press the putty into the cracks with the broad side of the putty knife. Smooth the putty out as best you can until the sill looks like one level surface.
Caulk the edges of the sill where it meets with the window trim using a caulking gun and a tube of exterior caulk. Allow the putty and caulk to dry for 24 hours.
Sand the wood putty filler with the 120-grit sanding block until the sill is smooth. Dust the sill with the dust brush. Go over it with a tack cloth to remove the finer debris.
Dip a paintbrush into a can of exterior stain-blocking wood primer paint. Paint the window sill by moving the bristles of the paintbrush back and forth over the wood. Wait 24 hours for the primer to dry.
Sand the primed window sill with the 120-grit sanding block. Do this lightly to avoid sanding off the primer. Sand it enough to smooth any rough spots. Dust the window sill with the dust brush and then apply another coat of primer paint. Wait 24 hours for the primer to dry.
Apply a coat of finish paint with the paintbrush the same way the prime was applied. Wait 24 hours and then apply a second coat.