Is it before or after your application has been accepted?

You pay when you submit the application at the end of the process on the site. 

In answer to your implied question, if you submit an application which is subsequently denied by the embassy, the application fee is lost.

But does the embassy outright reject a visa application or does it work with you to fix any deficiencies, such as missing documents or information?

50 minutes ago, 10years said:

But does the embassy outright reject a visa application or does it work with you to fix any deficiencies, such as missing documents or information?

That appears to vary.

Or, as a friend of mine found out in  January . Applied in France , all in order, due to delays, he had to leave without it. Which I why I didn’t get a visa and came exempt. So we both stayed 2 months instead of 3. He’d applied early but it apparently took 6 weeks. And yes, I know January was still difficult times , Thai Pass / insurance etc was easy compared to an evisa !!! 

2 hours ago, Toby1947 said:

The usual Thai scam. Pay before your visa is approved, if not approved goodbye application fee. Would you expect anything else from these villains in the Land of Scams

If you apply correctly, provide the correct documents a very few would have any reason for rejection. Despite several post of rejection on this site, there's generally more to the story about rejected applications that isnt told, in my experience.