Berlin to Amsterdam by train or plane?

Either method can be pretty cheap if booked in advance. Train time is 6.25 hours between city centers. For some cities, local transport to and from airports adds more time and expense to the flight, but Berlin and Amsterdam airports are both more convenient than average. See also www.skyscanner.com (tickets for sale now) and the DB German rail link (tickets sold from 3 months out).

I would check on a cheap flight! Last year we took the train and got stuck on route back from Amsterdam to Frankfurt due to train issues and it took us over 9 hrs to get back. The other Issues are the refugees crisis. Full trains and when you check on the german rail site they are even posting the issues right now due to refugees. Now this could change in April but we just bought a ticket Frankfurt/ Venice by Ryanair flight is 1 hr. for 13.95 Euros. Cant get any cheaper then that!

That is one route that I would probably choose flying instead of the train because the airports are easily accessible and not too far from the city centers.

I've travelled the Amsterdam - Berlin route and my suggestion would be train. It will be a more pleasant and relaxing trip rather than dealing with the usual annoying airport hassles, and you won't have to deal with extra charges for luggage. Even if the trip by train takes slightly longer, I'd still choose that over air travel on that route.

With sufficient advance purchase (up to 92 days), the Bahn will sell you a Europa-Spezial ticket for one from Amsterdam to Berlin starting at 39€. It doesn't look like most low-cost airlines service this route.

As for time, remember, the flight time might only be 1½ hrs, but you still have to get to and from the airports, check in, go through security, get to the gate, board, deplane, and find ground transportation, whereas the train goes between city centers.

The train, of course. Takes about the same time as flying, but is so much more relaxed and as bonus you get the landscape of Northern Germany free of charge.
It is hardly imaginable that this train route will be affected by the present massive refugee influx, if that still would go on April next year.

We opted to fly.
Took cab at about 7:15 AM to Berlin airport from Mitte- easy check in at airport and we did check luggage- arrived Amsterdam 10:35.
Took Bus 197 that dropped us off just steps to our hotel. We were sightseeing in Amsterdam before 1:00.
5 hours or so total transit- and it did not take up major part of a day as the train will.
If you have lots of time- train is fine- if not fly.