The St. Lucie County Canvassing Board voted 2-to-1 in favor of the recount late Friday, hours after a circuit judge declined to order one in the 18th Congressional District race.
Three days of early-voting ballots in St. Lucie were already recounted last week.
The remaining five days will now be processed beginning Saturday morning.
The board declined to order a recount of absentee ballots, which the Republican congressman's campaign had sought.
Attorneys for Murphy fought the recount, which isn't mandated under state law because of the margin.
Murphy is the unofficial victor in the race, with a lead of about 1,900 votes.