How do I prevent this kind of goal?

We have a goal kick, long kick to half-way line, their midfielder wins the header which puts the striker through one on one. It must happen to me 10 times a season (managing in the lower leagues).

Any idea how I can prevent this happening?

Set your keeper to short distribution so that he throws it out to one of your FB instead.

Yeah I always let my GK play it rather short to the FB/WB than long into the middle of the pitch. It also helps starting a nice quick wing attack

I play in the lower leagues, and I score plenty of goals just like that too. Tall guys (well high jumping guys) in centre midfield are always handy at that level. As mentioned, setting your keeper to pass it to a fullback will help, or otherwise perhaps get a keeper with a higher kicking attribute (so he can kick the ball further) or perhaps even getting some more aerially dominant centre mids are all options.

Deeper back line would surely mop up the headers too?

no the deeper line doesnt help. set to short distribute and get center backs who are as fast and strong as you can. that is the only solution i have found. happens to everyone.

Thanks everyone. I need to make it clear that this is from a goal kick situation, not when the keeper has it in his hands. I'll try telling him to play even shorter and see if he'll do what I tell him.

TRy getting him to pass down the flanks, setting him to 'sweeper keeper' or playing with a sweeper.

The 'ball over the top' is a goal I concede a LOT when things aren't going right for me and is hard to stop.

You should get a tall defensive midfielder. That is very helpful!

I set distribution to "defender collect", which helps; it's also something that disappears at the higher mentalities (control/attacking), because you're trying to build from the back. That's counterintuitive in a way, but it seems to be true; the "play from the back" shout might also help.

It also helps if you have a big guy in midfield, but in the lower leagues beggars can't really be choosers and that's hard to guarantee.