Writing in the FIFA Weekly magazine
published by world football's governing body, Blatter described the situation as one that "cannot continue."
Iran's ban was put in the spotlight at the Asian Cup in Australia earlier this year, when thousands of female Iranian fans watched their team without restriction.
At the match against Iraq, activists unfurled a banner showing the face of Ghoncheh Ghavami, a British-Iranian woman jailed for trying to watch a volleyball match against Brazil in 2014, and called for the ban to end.
The measure was imposed following the 1979 Islamic Revolution because the idea of mixed crowds was deemed un-Islamic.
Iran is in the running to host the 2019 edition of the Asian tournament, for which the United Arab Emirates is also bidding. But the ban is widely expected to scupper its chances of securing the event.
Blatter wrote: "I raised the topic at my meeting with the President of Iran, Hassan Rouhani, and came away with the impression that this intolerable situation could change over the medium term.
"However, nothing has happened. A collective stadium ban still applies to women in Iran, despite the existence of a thriving women's football organization.
"This cannot continue. Hence my appeal to the Iranian authorities -- open the nation's football stadiums to women."
During last year's football World Cup, CNN reported
how fans in Iran gathered to watch games in venues that defied a ban on public screenings.
At one coffee shop in the capital, Tehran, the tense game against Argentina -- a game Iran lost only to an injury-time Lionel Messi goal -- was watched by a large mixed crowd.
"100 percent it's better this way," said Negar Valayi. "It doesn't happen often. It would be great if we have more of this."
"It's actually much better to watch it with a bunch of people around because it makes you feel more excited," said Roya Marzbahan.
Hoardings advertising the World Cup throughout Tehran that summer had featured no pictures of women.
And state TV broadcasts of matches employed a delay of several seconds in order for images of female fans deemed too racy to be censored.
Blatter also hit out at football's continental confederations for failing to elect any women onto governing body's executive committee.
The committee includes three women -- one of whom has voting rights and two of whom are co-opted -- but they are elected directly by the FIFA congress following a change to the statutes in 2011.
"This was hard work because the members of FIFA's executive committee are elected by the national associations... and there was never, never a proposal for a woman to be finally in FIFA," the 78-year-old said at an event in Switzerland.
"We had to take the decision, and I did it in 2011 at the end of the congress, [that] we must have at least one woman on the executive committee."
He described football as a "macho" sport and warned: "We should change in the future."