Walker, 71, of Alloa in Clackmannanshire, was convicted of a string of domestic abuse offences against his ex-wives but had refused to resign his seat despite pressure from campaigners and MSPs, many of whom signed a petition calling for him to go.
In a dramatic statement tonight he said a "media onslaught" had made it impossible for him to continue.
He said: "It has been increasingly difficult for my wife and my staff to deal with the media interest in my case. That same media onslaught has also made it impossible to properly represent my constituents and their interests.
"My trial process on domestic abuse charges still continues at Edinburgh Sheriff Court with the sentence not due to be announced until September 20 after the receipt of the reports ordered by the court. However, circumstances have made it very difficult to continue as MSP, hence my decision to withdraw now."
The Dunfermline MSP was found guilty following a trial at Edinburgh Sheriff Court last month.
He carried out the attacks against his three ex-wives and a stepdaughter between 1967 and 1995.
The former SNP MSP, who was ejected from the party when the allegations surfaced, denied the charges.
His refusal to step down had sparked anger among the public and politicians with 93 MSPs signing a petition calling for him to resign.
The maximum sentence he could receive later this month is one year in prison. Under the law, only politicians sentenced to more than a year in jail are disqualified, so Walker could not have been forced out of parliament.
The 71-year-old did face having his wages curtailed if he was jailed. The Scottish Parliament's corporate body said 90% of his salary could be lost leaving him with £5,800 if he held his position while imprisoned.
In the statement released tonight Walker said it had been a "pleasure" to serve his constituents since May 2011.
He added: "As several other serving members of the parliament have bravely tried to point out, the court proceedings have not yet concluded.
"After September 20, there will be an opportunity for me to consider whether there are grounds for appeal and, under legal advice from my solicitor, I shall be making no further comment at this stage."
As a constituency MSP Walker's resignation means a by-election will be held in Dunfermline.
Scotland's First Minister had called for the Scottish Parliament to be given the power over the disqualification of MSPs.
The Scotland Act gives it the power to set out pay provision, meaning changes could be made by MSPs without referring to Westminster, but disqualification of a member is a matter for the UK Parliament.
Alex Salmond, who had called on Walker to resign, has written to Deputy Prime Minister Nick Clegg urging action and believes the powers could be devolved relatively quickly.
Scottish Secretary Michael Moore had also called for talks with the Scottish Parliament regarding the situation and tasked UK Government officials to explore possible solutions.
Scottish Liberal Democrats leader Willie Rennie, who put forward the petition calling for Walker to resign, said: "Good. Bill Walker should have understood immediately the gravity of his situation but it has taken 16 days for the penny to drop.
"It is sad that he continues to blame others instead of taking responsibility himself for his own actions. It would have been wrong for someone convicted of so many counts of domestic violence to return to Parliament. I'm pleased he's gone.
"The uprising of revulsion from people and Parliament against domestic violence is one of the satisfying features of this sorry episode.
"The message is clear: we will not tolerate domestic violence."
Scottish Labour's Claire Baker said: "I am pleased that Bill Walker has finally done the right thing and resigned.
"The people of Dunfermline deserve better and each day he remained an MSP was an affront to Parliament and democracy."
An SNP spokesman said Walker's position was "untenable".
He added: "People across the political spectrum have been demanding that he resign his seat, and it is right that there will now be a by-election so that the people of Dunfermline can elect a new MSP."
A spokeswoman for the Scottish Parliament said: "The Presiding Officer has received the resignation of Bill Walker, effective from Monday.
"There will now be a by-election in Dunfermline and she will consider when that will take place and notify the political parties in due course."