Although you can visit ancient Troy and/or the Gallipoli battlefields from Istanbul in one day, I don't recommend it.
The drive (or bus ride) is 4-1/2 hours each way (map).
If you simply must do it in a day, here's how:
As soon as the Istanbul Metro starts running (about 06:00 am), go out to the Büyük Istanbul Otogar (bus terminal) and find a bus to Gelibolu (for the Gallipoli battlefields) or Çanakkale (for Troy). More...
For Gallipoli, when you arrive in Gelibolu, consult the bus schedules for return trips to Istanbul so you'll know when you must get back to the bus station for the return journey. Then, negotiate with a taxi driver for a tour of the battlefields, specifying exactly the places you want to visit, how long you want to stay there, and for your return to Gelibolu by a specific time.
For Troy, when you arrive in Çanakkale, consult the bus schedules for return trips to Istanbul so you'll know when you must get back to the bus station for the return journey.
Then negotiate with a taxi driver for the 30 km/19 mile trip to Troy archeological site, an hour or two of waiting time, and the return trip to the bus terminal. (Yes, this is a bit expensive, but if you want to do this excursion in a day, you'll have to bear the cost.)
After your visit to the ruins, take your taxi back to Çanakkale, and catch your bus for the 4-1/2-hour ride back to Istanbul.
The entire excursion may take 14 to 16 hours, with about three to four hours at the Gallipoli battlefields, or two hours at Troy.
This trip is a bit faster if done in a rental car, but to really enjoy the trip, you should stay overnight in or near Çanakkale or, even easier, sign up for a guided tour.
—by Tom Brosnahan