One pilgrim has been arrested after clashing with anti-pope protesters on the route of the pilgrim walk in Sydney.

The pilgrim, from Newcastle, allegedly jumped on a gay protester and punched him in the neck. He was not charged and was released shortly after the incident.

About 1,000 protesters took up positions alongside the pilgrim walk for a rally against the Pope's opposition to homosexuality and birth control.

Chanting "Pope go homo, gay is great" and singing "Pope is wrong, put a condom on", the protesters threw condoms at the pilgrims, who were making their way to Randwick racecourse for an overnight prayer vigil.

A drag queen dressed in pink going under the moniker "Pope Alice" also paraded before the pilgrims, while other protesters wore T-shirts with slogans such as "Thank God I'm an atheist" and "Bless me father for I am a homo".

There was a heavy police presence at the protest, including officers on horses, and demonstrators were cordoned off from the bulk of the worshippers.

Most of the pilgrims reacted with smiles, waves and chants of their own but not all were happy about the protesters' presence.

The pilgrims, who were attending the prayer vigil ahead of a papal mass Sunday involving an estimated 500,000 people, appeared unfazed by the protest, with some making peace signs as they passed by.

Maraget Leatuafi from New Zealand said pilgrims had been advised by World Youth day organisers not to retaliate if the protesters challenged their faith.

"They are allowed to have their say too about what they believe but maybe they need to do a bit more study (about the church)," the 55-year-old said.

Another pilgrim, Ruud, 15, from the Netherlands, said he was not bothered by the protest.

"It is is their right to stand up for their views. we live in a democracy," he said.

Around 500,000 pilgrims are expected to be at the racecourse for tonight's vigil and tomorrow mass.

The Harbour Bridge was re-opened to traffic at 5:00pm after it was closed for the path of the pilgrimage.

- ABC/AFP