Why is my motherboard fan turning on and off every few seconds?

Are you sure it's the motherboard fan? It could be the CPU cooler's fan or even the case fans. You might want to check which specific fan is acting up. Once you identify it, that would help narrow down the issue.

If it's the CPU cooler's fan, try removing it and reapplying thermal paste. Sometimes air pockets can cause overheating, which makes the fan flip on and off. Just ensure you clean off the old paste before applying new.