You can take the 06:45 am High-Speed Train from Istanbul(Pendik) to Eskişehir, arriving at 09:37 am, then change trains to the Pamukkale Ekspresi which departs Eskişehir at 10:00 am, stops at Kütahya (11:35 am) and Afyon (13:26/1:26 pm), and arrives in Denizli at 17:56 (5:56 pm).
From Denizli, the Pamukkale Ekspresi departs at 08:00 am, departs Afyon at 12:33 pm, and Kütahya at 14:38/2:38 pm. At Eskişehir it arrives at 16:06/4:06 pm, in time for the 16:41/4:41 pm High-Speed Train departure for Istanbul, arriving at 19:25/7:25 pm.
So…it takes nearly 12 hours to travel by train what could be traveled by bus in 11 hours, and by plane in one hour.
But consider this: Denizli’s Çardak Airport is 64 km (40 miles) east of the city, so you must allow several hours for the transfer from Denizli or Pamukkale to the airport, including security checks and check-in time; then the flight, baggage claim, getting to ground transportation, and at least an hour to travel from Istanbul‘s Atatürk Airport to the city center, and probably two hours from Sabiha Gökçen Airport.
The train’s great advantages are comfort and a relaxing scenic ride through the fertile Aegean region.
—by Tom Brosnahan