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The Edinburgh South West MP explained her decision in a statement on Twitter, blaming issues over “transparency and scrutiny” in the party.
Her decision comes after Douglas Chapman resigned as the SNP national treasurer on Saturday.
In the tweet, Ms Cherry said: “I’ve resigned from the NEC of the SNP.
“A number of factors have prevented me from fulfilling the mandate party members gave me to improve transparency & scrutiny & to uphold the party’s constitution.
“I won’t be making any further comment at this stage.”
Mr Chapman, MP for Dunfermline and West Fife, said he was not given enough information to do the job.
Deputy First Minister John Swinney was forced to deny that Police Scotland was investigating “£600,000 of SNP funds that was raised by activists and campaigners and perhaps diverted elsewhere?”, telling the BBC: “Not to my knowledge, no.”
He told BBC Scotland’s The Sunday Show: “I don’t understand quite what’s prompted this.
“The National Executive Committee has responsibility for scrutinising the party’s finances… and in addition to that, the accounts of the party are independently audited by external auditors and are submitted to the Electoral Commission for scrutiny.
“So there’s a huge amount of scrutiny of party finances that goes on.”
Mr Chapman took over the role last year, while Ms Cherry only recently returned to politics after taking a break for health reasons.
It remains unclear what led to Mr Chapman’s decision, but SNP business convener and fellow MP Kirsten Oswald said she “fundamentally disagrees” with Mr Chapman’s assessment.
Labour MP Ian Murray suggested the SNP is “in crisis”.
The shadow Scotland secretary said: “Losing one member of your National Executive is careless.
“Losing three members of your finance committee, your treasurer and a member of your National Executive probably indicates a party in crisis.
“The SNP have long been gripped by a kind of centralism and secrecy that would make Lenin blush.
“From the failure to provide basic answers on what an independent Scotland would use as a currency, to the radio silence on what is going on in the party’s bank account – the people of Scotland deserve answers now.”
More to follow…
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