I would say 頭痛は治まった when my headache is gone.
You can say 頭痛が消えた too and I think it might match with your English.
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Sentence textLicense: CC BY 2.0 FR
This sentence was initially added as a translation of sentence #1046405
added by marcelostockle, October 7, 2011
edited by marcelostockle, October 8, 2011