The tune, a parody of the song "My beloved homeland, my great homeland," first aired Friday on Youssef's TV show "Al-Barnameg," Ahram Online reported.
Since then, it has been viewed on YouTube more than 200,000 times.
In the song, Youssef criticizes Egypt's dependency on money from Qatar with lyrics such as "My beloved Qatari, the youngest brother ... Every day your money doubles-up ... His investments fill his life ... The Qatari spends and shows off.
"Oh Qatari, who's filling our pockets ... Oh a disaster that's brought down our flag ... Oh a renaissance [a development project announced by the Brotherhood] crushing our people ... This is what the Brotherhood gave us ... Sell Egypt wholesale and retail ...," the song went on.
"My beloved homeland" was first released in 1960 as a song that advocated for Arab unity and solidarity.
"We do not have a problem with Qatar as a country. The problem is that when someone comes to rule this country, the first thing they think of is to seek aid," Youssef said.
Meanwhile, an Egyptian court has thrown out a lawsuit seeking to have Youssef's show banned from television, the BBC reported.
The lawsuit was filed by a Muslim Brotherhood lawyer over allegations that Youssef used his weekly program to insult President Mohamed Morsi and Islam.
Prosecutors are looking into complaints that Youssef allegedly insulted the president and Islam on his show.