Mr Ferydoun failed to meet the bail terms on unspecified financial issues and was taken to prison.
He has previously been linked to officials at the centre of a scandal involving inflated salaries for managers at the state insurance firm. He has always denied any wrongdoing.
The saga has dogged President Rouhani for more than a year.
The judiciary spokesman, Gholamhossein Mohseni-Ejeie, said: "Multiple investigations have been conducted regarding this person [Mr Ferydoun], also other people have been investigated, some of whom are in jail.
"Yesterday, bail was issued for him but because he failed to secure it he was referred to prison."
Mr Ejeie said Mr Ferydoun would be "released once he provides the bail".
It has not been made clear on what charges Mr Ferydoun has been detained.
The so-called "payslip scandal" began in May last year, when salaries of top managers started making their way into the public domain. Some were around 50 times the minimum public sector wage.
The saga has been a major blow to the reputation of the government of President Rouhani.
Mr Rouhani was re-elected for a second term in May. in the first round of voting, taking 57%.
But during the election campaign he came under fire for his policies on corruption.
In a heated TV debate, Mr Rouhani was accused of blocking an inquiry into corruption charges against relatives.
It was also alleged some of his ministers were linked to illegal imports and that the president had received heavily subsidised public properties.
The brother of Iranian President Hassan Rouhani, Hossein Ferydoun, has been detained, a judiciary spokesman says.