To reach Guadalajara from Madrid Airport, you must first take the metro. Line 8 will take you to the Nuevos Ministerios station in about 20 minutes. Here you can take a RENFE Cercanías (suburban) train directly to Guadalajara.
Trains start at around 5:58 and run until approximately 22:57. A single journey ticket costs between €6.10 - €27.20 each way as there are different trains going to and from Guadalajara and the journey time is ranges from approximately 25 minutes to 40 minutes, the metro costs €1.50 per journey.
For information and reservations call RENFE on Tel: +34 90 232 0320