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We are a married couple, a US citizen and a non-resident alien (a J1 visa holder). Our child lives with us. Presumably, the US citizen is eligible to file as a head of household since she's considered unmarried for tax purposes (source).

But then there's the requirement that the head of household should pay more than %50 of the expenses. We pay the expenses from our joint account. The US citizen has higher income, so effectively she's paying more than %50. But unfortunately, the major bills (rent, daycare) are under the name of the non-resident alien.

So is the US citizen eligible to file as a head of household or not?

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So is the US citizen eligible to file as a head of household or not?

If they meet the requirements they are eligible regardless of who's name is on what account/bill. The name on a bill/account doesn't change where the support came from. In the unlikely event that the IRS requires them to prove eligibility, the higher income going into a joint account that is then used to pay the bills should be perfectly adequate to prove more than 50% support.

Curiously, I came across this IRS article that seems to indicate you could also choose to file jointly:

If, at the end of your tax year, you are married and one spouse is a U.S. citizen or a resident alien and the other is a nonresident alien, you can choose to treat the nonresident as a U.S. resident.

I'm not sure of all the implications, but might be worth investigating.

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