The high court on Monday found Mrs Hanse-Himarwa guilty of corruption and corruptly using her office for gratification.
She also used her former position as Hardap governor in 2014 when she placed some of her relatives on a list of housing beneficiaries under the country’s mass housing initiative.
President Hage Geingob has accepted the resignation.
The presidency said due to the guilty verdict and in line with Mr Geingob’s commitments toward transparency and battling corruption, he would have been left with no option but to relieve Mrs Hanse-Himarwa of her ministerial duties.
Mrs Hanse-Himarwa, in a statement released by the education ministry, said she understands “the seriousness of the conviction” and is “mindful of the president’s strong views on transparency and accountability.”
Before being appointed as education minister on March 20, 2015, Mrs Hanse-Himarwa was governor of Hardap region.