‘Entree’ is more upscale. You buy an ‘entree’ in a better restaurant where you have a meal of many courses. Lower cost or traditional restaurants might use ‘main course’. The recent trend is for restaurants, especially those with smaller menus, to not categorize the food at all. I would never use ‘entree’ to refer to a main course that I cook at home. I’d always say ‘main course’.

They pretty much have synonymous meaning/usage, but it might depend on region. I would probably use entree. But, if you use either of them, it wouldn't sound strange.