The rare display of public dissent came after a call for protests by Mohamed Ali, a building contractor and actor who has accused the president and the military of corruption.
Before fleeing to Spain where he now lives in self-imposed exile, Ali says the company he managed implemented projects for the military for 15 years.
He has said his work gave him a close look at the way funds have been handled.
In a series of videos posted online, Ali has accused el-Sisi and the army of wasting millions of dollars of public money on palaces, villas and hotels.
“Your time is up,” Ali said, addressing el-Sisi in a video posted on Tuesday, telling Egyptians to go to the streets on Friday.
For his part, el-Sisi told a youth conference last week that the allegations of corruption within the army and the government were “lies and slander” and amounted to defamation.
Public attention shifted to Ali after he began posting videos earlier this month, accusing Egyptian officials of squandering billions of Egyptian pounds. His first video on September 2 garnered 1.7 million views on his Facebook page alone.
Since then, dozens of cartoons have been made in Egypt pitting him against el-Sisi, as well as images depicting Ali as another Mohamed Ali, an Ottoman-era commander who ruled Egypt in the 19th century.
“Mohamed Ali is probably the most popular man in Egypt right now,” Mohamad Elmasry, chair of the media and journalism programme at the Doha Institute for Graduate Studies, told Al Jazeera.
“Millions of people have watched his videos, while his anti-Sisi hashtags have gone viral.
“This is something that is a legitimate threat to the el-Sisi government – if it wasn’t a legitimate threat, then el-Sisi wouldn’t have come out and responded directly to Mohamed Ali at last week’s youth conference,” said Elmasry, adding it was “unprecedented” for el-Sisi “to be put on the defensive like that inside Egypt by an Egyptian”.
Egypt outlawed all unauthorised demonstrations in 2013 after el-Sisi, as defence minister, led the military’s overthrow of democratically-elected President Mohamed Morsi following mass demonstrations.
Since then, Egyptian authorities have imprisoned and prosecuted thousands of people, according to human rights groups, with a nationwide crackdown intensifying after el-Sisi was first elected in 2014 with 97 percent of the vote.
Some Egyptian activists have warned of the dangers that protesting can have on the lives of demonstrators, given what they called a tight grip on security by authorities.
Ali has also demanded the release of all political prisoners in addition to army and police officers arrested for opposing the president. He also urged security forces not to confront the protesters but to protect them.
El-Sisi’s supporters say dissent must be quashed to stabilise Egypt and also credit him with economic reforms agreed with the International Monetary Fund.
The introduction of harsh austerity measures might have helped to reboot an economy battered by the 2011 Arab Spring but has also resulted in the poverty rate soaring.
According to official statistics, released in July, one in three people in Egypt – a country of some 100 million people, is living in poverty. Other estimates put the number much higher.
Elmasry said that even though Egyptians have been aware of the corruption within the government apparatus, the fact that Ali “is an insider who worked with the military for about 15 years, that he has intricate details and also the fact that economy is spiralling out of control for the average Egyptian” appears to have struck a chord with many disenchanted people in the country.
“People … were looking for some kind of a spark, and Mohamed Ali has given that to them.”