Volker has served in the special representative role since 2017 on part-time basis, in an effort to help Ukraine's government resolve a years-long confrontation with militant separatists in the country who are sponsored by Russia.
On Thursday, a whistleblower complaint from within the intelligence community became public, and in it Volker was described as trying to "contain the damage" from efforts by Trump's lawyer Rudy Giuliani to press Ukraine to investigate Democrats.
One of the sources who spoke to NBC News said that stepping down as special representative will allow Volker to be freer in what he can say should he be called to testify before Congress about the Trump administration and Ukraine.
That source said Volker has emphasized to his colleagues at his other ventures outside the government that he was trying to build a firewall between his government work and his other work, in order to protect the latter.
Neither Volker nor the State Department responded to requests from NBC News for comment.
Congressional Democrats are conducting an impeachment investigation of Trump and have sought testimony from Volker relating to a July 25 phone call in which Trump encouraged Ukraine's president to investigate Democratic presidential candidate Joe Biden and his son.
Stock markets have so far largely shrugged off the impeachment inquiry.
Even if the Democrat-controlled House of Representatives were to impeach Trump, he would not be removed from office unless the Republican-controlled Senate found the president guilty.
Volker's resignation was first reported by the State Press, a student-run publication at Arizona State University.