Richard Burr of North Carolina said he had decided to do so because he did not want the investigation to distract the committee from its work.
Mr Burr's phone has been seized by the FBI as part of the inquiry.
The senator, who denies wrongdoing, allegedly used inside information to avoid market losses from coronavirus.
He declined a request for comment.
Mr Burr and his wife sold as much as $1.7m (£1.4m) of equities in February, just before markets plunged on fears of an economic crisis.
It is illegal for members of Congress to trade based on non-public information gathered during their official duties.
Republican Senators Kelly Loeffler of Georgia and James Inhofe of Oklahoma, as well as Democratic Senator Dianne Feinstein of California, also reportedly sold holdings before the downturn, but are not confirmed to be under investigation.
Ms Feinstein said she had answered questions from the FBI regarding trades made by her husband, however.
Republican Senate Majority Leader Mitch McConnell said Mr Burr had contacted him to inform of his decision to step aside temporarily.
"We agreed that this decision would be in the best interests of the committee and will be effective at the end of the day tomorrow [Friday]," Mr McConnell said in a statement.
Mr Burr said: "The work the Intelligence Committee and its members do is too important to risk hindering in any way. I believe this step is necessary to allow the Committee to continue its essential work free of external distractions."
He turned over his mobile phone to authorities after federal agents issued and executed a search warrant at his Washington, DC, home.
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