Alex MacLeod, 20, who represents Caithness and worked for First Minister Alex Salmond on leaving school, said he had to be “honest about any mistakes that I have made” in his letter of resignation.
Earlier this year he was reported by police to the Procurator Fiscal in connection with alleged offences under the Representation of the People Act 1983.
He is due to appear in court next month.
In a statement, he said: “Today I have notified the Chief Executive of my intention to resign from the Highland Council, effective from 30th September 2013.
“I have received notice of a charge of electoral misconduct, and I intend to step aside from my Council role so that I can work with the my solicitor to reach an acceptable solution.
“I need to be honest about any mistakes that I have made, and face the consequences of my actions. I got into this situation when I was very young, with all the arrogance and hot-headedness that that entails.
“I feel a redoubtable sense of sorrow and regret for the events which have unfolded. I understand that this news will hurt a great many of my friends, colleagues, and supporters. I am truly,very genuinely sorry about that.
“My biggest apology is to the people who voted for me. It is right that they now have the opportunity to elect a new councillor in a by-election. Following legal advice, I cannot offer any further comment at this time.
Mr MacLeod was the Highlands’ youngest councillor at just 20 years old.
He stood down as an SNP Party member when the allegations arose.
Mr MacLeod, who worked for First Minister Alex Salmond on leaving school, was only 19 when he won his Landward Caithness seat in May’s Highland Council elections.
He was Gaelic spokesman for the SNP-led administration, but has resigned from the controlling group on the local authority while there are legal proceedings against him.
A conviction under the Representation of People Act 1983 can carry a maximum six-month prison term.
A police probe was launched when a complaint was made to the force by an unnamed individual about his conduct during the election campaign.
It is understood part of the investigation centred on accommodation expenses.
A Highland Council spokesman: “We can confirm that Alex MacLeod has intimated by email his resignation from the Council with immediate effect. A by-election must be arranged within three months of his resignation.”
A Crown Office spokesman said: “We received a report concerning a 20-year-old male, in relation to a number of alleged incidents said to have occurred between 15 March 2012 and 8 June 2012.
“The case is live for the purposes of contempt and it would be inappropriate to comment further.”
Mr MacLeod was born and raised in Tain, Ross-shire, and was taught through Gaelic at Tain Royal Academy. He left school early and worked for 10 months for First Minister Alex Salmond.
He subsequently studied Law at Edinburgh University and was also very active in the Young Scots for Independence organisation, rising to the position of National Secretary.
In 2010 he was appointed a Parliamentary Assistant to the SNP MSP Rob Gibson and and was his Campaign Manager in the 2011 election when Gibson captured the Caithness, Sutherland and Ross seat from the Lib-Dems.
He has enjoyed a high profile on the authority since his election victory, declaring the council would “not know what hit it” once he started work.
The councillor was a vocal supporter for the lifting of the ban on same-sex marriage saying: “I look forward to making full use of this new law – maybe a wee bit later in life.”
Spending limits are imposed on election candidates so that wealthy individuals cannot lavish huge amounts of cash on winning by splashing out on heavy advertising or sponsorship.
A councillor can be disqualified if they have been found to have submitted a misleading record of expenses.
The limit for Mr MacLeod’s ward was £1226.04 but the expenses shows he spent £88.46 less than the maximum permitted.
Mr MacLeod is also a board member of Eden Court Theatre and Caithness Citizens’ Advice Bureau, and represents the Highland Council on the Dounreay Stakeholder’s Group.