Club president Josep Maria Bartomeu told reporters there had been "a mistake... in tax planning" in connection with the transfer.
Barcelona had been accused of tax fraud over the signing, which it denied.
Neymar and his father are also being investigated over alleged tax fraud, which they also deny.
"We have had to accept paying a €5.5m fine due to a mistake in the 2011 and 2013 tax planning in the signing of Neymar," Mr Bartomeu said.
"It was better to accept this agreement than continue on with the uncertainty that has dragged on for a long time over the Neymar case."
Barcelona made a voluntary tax payment of €13.5m in 2014 after being charged with tax fraud over the signing, but denied any wrongdoing.
Neymar, whose full name is Neymar da Silva Santos Junior,  joined Barcelona in June 2013 after a successful career with the Brazilian club, Santos.
Barcelona said it paid €57m (£43m) for the forward, with the player's parents receiving €40m and Santos €17m.
But investigators said the fee was closer to €83m and that Barcelona had concealed part of the deal. The club denied the claim.
Earlier this month, Spanish prosecutors called for Neymar to be tried for fraud.
They allege that the player and his father hid the true value of the transfer from Santos to Barcelona.
A Brazilian investment fund, which held 40% of Neymar's sporting rights when he played at Santos, argues it was deprived of its full share of the transfer deal.
Neymar is also being investigated for tax evasion in Brazil.
Barcelona football club has agreed to pay a €5.5m (£4.3m) fine over the transfer of Brazil international Neymar in 2013.