Skinner, who is performing his Man in a Suit stage show at this year's Edinburgh Festival Fringe, said if he was living in Scotland he would be a Yes voter.
The author and writer of the famous Three Lions football song, said that if England was voting to separate from the rest of the UK he would be a No voter.
Skinner, 57, said it is "difficult to say you are proud to be English because you are seen as bit of a fascist".
He likened England to "cordial" of right-wing politics that needed diluting by its union with Wales, Scotland and Northern Ireland.
Skinner said he feared England alone will become embroiled in extreme politics if it was not for the influence of politics elsewhere in the UK.
He added: "I have thought about the referendum a lot, and it's interesting for an Englishman to put himself in the place of a Scottish voter.
"It is difficult to say you are proud to be English because you are seen as a bit of a fascist, but in Scotland it seems that patriotism is a pure and romantic thing and because of that I envy the Scots.
"All my political decisions are romantic... and if I was Scottish I would probably vote Yes.
"If there was a English independence vote I'd vote No, because it is far easier to talk about being British [than being English]."
Skinner noted that for him it feels uncomfortable to say he is "proud to be English" whereas Americans or Australians do not seem to have the same reticence.
He added: "I feel it is good for England to have that union with Scotland, Northern Ireland and Wales because they dilute this potentially fascist cordial.
"If fascism was a kind of Ribena it would add that dilution.
"I would be really sad if Scotland became independent.
"I'd be sad because we are a dysfunctional family but we have love between us. And of course the Fringe means a massive amount to me, and so does Edinburgh, my son was conceived there, just off the Royal Mile."
Skinner, along with David Baddiel and The Lightning Seeds, went to number one in the charts twice with the song Three Lions, which was originally written to support the England football team at Euro 96. England and Scotland played each other during the tournament, with the home side winning 2-0 at Wembley Stadium.
Skinner's one-man stand up show is appearing at the Assembly George Square Theatre from August 1 to 24.
His first appearance at the Fringe was in 1987 when he spent £400 of his last £435 in savings to book a room at the Edinburgh Festival Fringe.
He said one of his shows received no audience at all and the most he played to was an audience of 12.
However, four years later in 1991 he returned to the city and beat fellow nominees Jack Dee and Eddie Izzard, to win one of comedy's most prestigious prizes, the Perrier Award, now known as the Edinburgh Comedy Award.
He last toured the UK in 2007 with the Frank Skinner Live which included three "homecoming" gigs at Birmingham's NIA - he is from West Bromwich.
Skinner said this year's Fringe would be a different experience for him as he has a young son, Buzz.
He was recently in Edinburgh in his role as presenter of the Sky Arts Portrait Artist Of The Year 2014, which was shooting heats at the National Museum of Scotland.
"I am now a fan of the National Museum of Scotland, there is lots of interesting stuff there," he said. "It's not just Dolly the Sheep."