I'll be back after five minutes.
I'll be back in five minutes then.
Please check them. I am confused about "then" in the context.
kumenglish I'll be back after five minutes. Possible but odd. You will be back in five minutes, or you will be back after five minutes is up, or you will not be back until after five minutes.
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kumenglishI'll be back after five minutes.
Possible but odd. You will be back in five minutes, or you will be back after five minutes is up, or you will not be back until after five minutes.
kumenglishI'll be back in five minutes then.
"Then" is a sentence adverb and therefore has to have a comma: "I'll be back in
Those are both possible, but "in" seems more natural. There is no particular reason why "in" should be used with "then" and "after" without "then".
The word "then" most probably expresses that "I'll be back in five minutes" follows on as a consequence or result of something previously mentioned or apparent from the context. For example:
A: It's only a hundred yards down the road