Firstly, we know the train leaves King's Cross Station at precisely 11 o'clock on the morning of every September 1st and travels to Hogsmeade Station, which is somewhere in Scotland.
We also know from Scotlandinfo.eu that in Scotland the sun sets on September 1st at 8:19pm on average. The actual time is either later or earlier depending on where in Scotland Hogsmeade is located. Since September 1st is before the winter equinox (September 22nd or 23rd) the further north we get the later the sunset is going to be (although not by much since we are fairly close to the date of the equinox).
Finally, we know the train arrives in Hogsmeade on September 1st after sunset.
So in conclusion the train ride should be at least 9 hours long, but do we have a better estimate or know the actual time?