Hundreds of thousands of worshippers, beating their heads and chests in ritual mourning, pour into Karbala for the rite, many walking for hundreds of kilometres.
Several hours later a roadside bomb in the district of Doura, in southern Baghdad, wounded 12 pilgrims, an interior ministry source said.
Arbaeen is a Shia religious observation that occurs 40 days after the Day of Ashoura, the commemoration of the martyrdom of Hussein bin Ali, the grandson of Prophet Muhammad.
Thousands of troops and police have been deployed to protect worshippers as they walk towards the Imam Hussein shrine.
During a pilgrimage last February, a female suicide bomber attacked a tent
filled with women and children resting during the walk to Karbala, killing 40 people and wounding 60 others.
A month before that, a suicide bomber dressed in women's clothing and hiding among Iranian pilgrims killed more than three dozen people outside a mosque in Baghdad's Shia neighbourhood of Kazimiyah.
Saad Muttalibi, an adviser to the Iraqi council of ministers, told Al Jazeera that protecting the large number of pilgrims was always going to be a challenging task.
"It is almost impossible to protect six million civilians," he said referring to the pilgrims.
"The problem that we have is that the Americans have released a number of prisoners from their prisons straight into society without allowing the Iraqi government to do further interrogations to check to the validity of their innocence.
"The other problem is that the Iraqi security forces are not doing enough in combating terrorism in harder way."