Not in the way that the whimsical toys would lead you to believe. Starting around the turn of the century circuses around the US had special livestock cars built to handle exotic animals. The Ringling Brothers' current fleet are built from ex Union Pacific railway post office cars with special quarters for each animal type. Older cars used in the early 20th century were outside braced wooden livestock cars with side and end doors to unload animals.

You couldn't have giraffe heads poking out of the top of the car for numerous reasons, not least because transporting them in that fashion would cause them to suffocate from exhaust in tunnels and get injured by debris or low clearance obstacles. They were most likely trained to lay down, which would provide at least 8-10 feet of ceiling height.

You can learn more here: http://books.google.com/books?id=40oEAAAAMBAJ&pg=PA22&dq=ringling+giraffe+train&hl=en&ei=YPJQTt-eBMjLgQfFuLnkBg&sa=X&oi=book_result&ct=result&resnum=2&ved=0CDkQ6AEwAQ#v=onepage&q=ringling%20giraffe%20train&f=false