FARC, or the Common Alternative Revolutionary Force, is a political party spun out of the former guerrilla movement.
In a statement, the FARC said that its candidate, Rodrigo Londono Echeverri, alias "Timochenko," underwent open-heart surgery on Wednesday.
The group said that Timochenko would need several weeks to recover and would not be in fit state to run a campaign.
"Circumstances... about our candidate's recovery process, after receiving surgery yesterday, combined with those already discussed about the characteristics about an electoral participation, has led us to cancel our presidential aspiration," said the FARC.
The recently formed party after the FARC guerrilla group signed a peace deal with the government also called on the public to turn out and vote for FARC candidates in legislative elections on March 11.
"We invite (the people) to vote on Sunday, March 11, for our lists for the Senate and the Chamber," read the statement.
The group also reiterated its willingness to continue fighting for unity and reconciliation in Colombia.
"We express our willingness to dialogue with all political sectors in order to build bridges to make the perspective of a great national convergence into a reality," it sustained. "The common people will count on Congress...to work tirelessly for the proposals of democratic peace with social justice."
The FARC also called for the end of all politically motivated violence.