She was popular with the West for her efforts to bring Ukraine's banking system closer to international levels.
But she was also seen by some in Ukraine as a "Russian stooge".
Many banks were being run as glorified piggy banks for local billionaires.
The 52-year old is credited with allowing the local currency, the hryvnia, to find its own level, a move that saved the central bank from running out of money.
However, that move, undertaken on the advice of the International Monetary Fund, also cut the value of people's savings and introduced soaring inflation.
Local disapproval has prompted aggressive stunts, including a coffin being placed outside her house and the image of a pig wrapped in a Russian flag sprayed on her walls.
Some of her enemies suggested she should be jailed for her actions.
Ms Gontareva said her successor at the National Bank of Ukraine would also struggle against vested interests:  "There will be political pressure on anyone who has this job. For this reason, I would like to tell my successor: be strong."
Ukraine has been caught up in armed conflict since 2014, when Russia annexed Ukraine's southern Crimea peninsula.
Pro-Russian rebels later launched an insurgency in the east.
Ms Gontareva said her resignation had been submitted voluntarily.
The governor of Ukraine's central bank, Valeriya Gontareva, has resigned the post after three years, following intense pressure from tycoons whose banks she shut down for conducting illegal transactions and loans.