Mr Murrell, who is married to Nicola Sturgeon, gave the party a loan of £107,620 in June 2021.
The SNP had repaid about half of the money by October of that year.
When asked whether the party still owed him money, Mr Yousaf told journalists: "I think there is money still absolutely outstanding to Peter Murrell in terms of the repayment of the loan."
The first minister said he would lay out details of how much is owed after a review into the party's governance takes place.
Mr Murrell, who has been married to Ms Sturgeon since 2010, was in charge of running the party organisation for more than 20 years until he resigned last month.
He was arrested by police at the start of April over an investigation into SNP finances and questioned by detectives for 11 hours before being released without charge pending further investigation.
Police launched a formal investigation into the party's finances in July 2021 after receiving complaints about how donations made for an independence referendum campaign had been used.
The SNP raised £666,953 through appeals between 2017 and 2020 with a pledge to spend these funds on a future campaign.
Questions were raised after its accounts showed it had just under £97,000 in the bank at the end of 2019, and total net assets of about £272,000.
Last year it emerged Mr Murrell gave a loan of £107,620 to the SNP to help it out with a "cash flow" issue in June 2021, the month after the Scottish Parliament election.
The party had repaid about half of the money by October of that year.
Earlier on Thursday, Mr Murrell was seen in public for the first time since his arrest when he was spotted leaving the home he shares with Ms Sturgeon near Glasgow. Ms Sturgeon was seen later in the day also leaving the property.
Police spent two days searching the house earlier this month.
Ms Sturgeon has previously said she cannot recall when she first learned that her husband had loaned a six-figure sum of money to the party she led for more than eight years.
She added: "The resources that he lent to the party were resources that belonged to him."
On the same day as Mr Murrell was arrested, a motorhome was seized by police, which The Mail on Sunday reported had been sitting outside the Dunfermline home of Mr Murrell's 92-year-old mother since being delivered there in 2021.
The SNP has claimed that it was bought to potentially be used as a "campaign battle bus" ahead of the last Scottish Parliament election but was never used.
Ms Sturgeon's successor, Humza Yousaf, has previously said he was unaware that the party had bought the motorhome until he became party leader last month.
On Wednesday, Colin Beattie resigned as SNP treasurer after his arrest the previous day as part of the police investigation. He was also subsequently released without charge pending further inquiries.
Mr Yousaf responded to questions about the SNP's finances by saying: "We are definitely not facing bankruptcy, I'm pleased to say we are on a steady footing when it comes to the party's finances.
"I don't think parliament is the place to do a statement on the party's finances.
"I've, of course, instructed the governance and transparency review and when the report comes in on that review, I'll make that public."
He has resisted calls for Ms Sturgeon, Mr Murrell and Mr Beattie to be suspended from the SNP while the police investigation is ongoing.
During First Minister's Questions, Scottish Conservative leader Douglas Ross called on Mr Yousaf to make a statement to Holyrood on the SNP's finances.
He said there are "legitimate questions that the Scottish public deserves the answer to".
Mr Yousaf did not respond in the chamber to the calls for a statement, but told MSPs there are "serious issues" relating to the party which he will not "shy away from".