Yes, self-employment counts for the Dependent Care Deduction. When you get to the self-employment section, one of the first questions will be "Who did this work or owned this business" be sure that you answer that it was your husband that did the work. Also, when you get to the W-2 section, be sure that you answer that the W-2 belonged to you. This will tell the program and the IRS that you both had earned income.
The requirement is that you both have earned income. It doesn't have to be reported on the 1099-Misc, the Schedule C where you will report his income, based on your records, is all you need for him.
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