If you follow intermittent fasting traditionally, then you would want to include your protein powder within your eating window. For example, if you typically only eat for 8 hours during the day, then you would include it somewhere within that 8-hour time frame. Normally people following intermittent fasting don't consume any calories in their fasting window, and all protein powders do contain calories.
It's completely up to you though and how strictly you follow it. Within your eating window though, popular options to include your protein are after workouts, in between meals, part of a meal, etc. There isn't really a right or wrong answer here.