If you are emphasizing the need for a specific amount of time to pass, using ‘timer’ is more precise than ‘alarm’.
Put the eggs into the boiling water and set the timer for three minutes.
I set the alarm for 8:50 to remind me that I have an italki class at 9.
The paint isn’t dry enough to add a second coat. I set the timer for two hours an hour ago, so it should go off in an hour. Or ‘in an hour from now.’