His resignation takes effect on Sept 1.
Earlier, he said his dual role could pose problems given that the responsibilities of the Office of the Ombudsman, which is an independent organisation, include scrutinising the work of the NLA.
Appointed ombudsman on Dec 8, 2013, Mr Pornpetch has served eight months of his six-year term.
As well, the office will submit two candidates to join the National Reform Council (NRC), deputy secretary general Raksagecha Chaechai said on Wednesday.
They are Panit Nitithanprapas, the incumbent chief ombudsman, and Pichet Soontornpipit, a former ombudsman in office from 2000 to 2003.
Both have expertise in politics and the judicial process, Mr Raksagecha said.