The club has retired the number 18 jersey in tribute, and a friendly between Derry and Ballymena United scheduled for this evening at The Showgrounds has been cancelled.
The striker also played for Glenavon whose fans are planning a tribute at Saturday's Irish Cup game.
Hundreds of people including Sinn Fein deputy First Minister Martin McGuinness, the Derry City team and Glenavon boss Gary Hamilton attended the funeral at St Mary's Church, Ballybrack, in Co Donegal to pay their respects.
Irish President Michael D Higgins led thousands of tributes to the striker from across Ireland and the UK yesterday.
"They have come from all of those who have known of his great footballing career as an iconic star for Derry City FC," he said.
"His colleagues have correctly pointed to his great strength of character and his generosity as a colleague and club member.
"Those of us who attended the League of Ireland and had the pleasure of seeing his many appearances will recall his great skills and sportsmanship.
"They will be joined by the public in general in admiring his courageous battle against incredible odds and they will want to send their sympathy and solidarity to his wife and partner, Terri Louise Farren."
Northern Ireland manager Michael O'Neill also paid a warm tribute to the footballer.
Yesterday there were growing calls for the new stand under construction at The Brandywell to be named after Mark.
A petition calling for the gesture garnered more than 1,500 signatures in just a day.
Among those backing the move is SDLP leader and Foyle MLA Colum Eastwood.
Mr Eastwood said: "Mark Farren was incredibly loved in this city.
"The huge response to his tragic loss has shown just how deep that affection for Mark was.
"He was definitely one of the most loved Donegal men in Derry. He became one of our own. Our thoughts and deepest sympathies are with his wife Terri Louise and his wider family in Greencastle at this time.
"We all knew Mark to be a great goal scorer on the pitch, someone who would give everything to Derry City in good times and in bad.
"But the last number of years has also shown us something even more admirable.
"The bravery with which Mark bore his illness, much of it in the public eye, struck everyone in Derry. He showed a courage which remains an example to us all. Given Mark's huge stature at the club, it is natural that Derry City fans are thinking of ways to pay tribute to his legacy.
"I note that the club has already retired the number 18 shirt he wore and I think Liam Coyle's idea to name the new stand after Mark would be a further fitting tribute.
"Once built, it will be a small but important gesture to all that Mark meant to Derry City FC over recent years. For my part, I think it would be a great way to remember Mark. May he rest in peace."
A book of condolence has been opened at The Brandywell by the mayor of Derry and Strabane and the club.
Mayor Elisha McCallion said Mark's untimely death had a huge impact on the people of the city and the book would allow sports fans from all over the city to express their condolences and share their memories of Mark.
She added: "Mark was a true gentlemen in every sense of the word. He loved sport and was a real ambassador for soccer across the north west."
Derry City chairman Phillip O'Doherty said: "We offer our sympathies to his family. He was a superb player and I think the entire football community throughout Ireland would say the same. But, most of all, he was a decent human being."