The Islamic militants attacked Maiduguri, the biggest city in north-east Nigeria, in the early hours of Sunday morning forcing all churches to close their doors.
It's estimated that up to 45,000 Christians have been forced to flee their homes in Maiduguri because of the threat of Boko Haram.
The group is attempting to set up an Islamic caliphate by taking over parts of Nigeria.
Military officials said hundreds of militants died in clashes yesterday.
Senior officers told reported the extremists were "everywhere" and had surrounded the town before retreating later in the day.
The army claims it recovered weapons including artillery guns and rocket-propelled grenades.
WHAT IS BOKO HARAM?
• Created in 2002, declared terrorist group in 2013
• Name means 'Western education is forbidden'
• Attempting to create Islamic State
• Thousands killed, millions affected.
Nigerian fighter jets were also seen in the skies dropping bombs which damaged some homes.
Up to eight civilians were killed during the day.
Revd Canon Hassan John from the Diocese of Jos in Central Nigeria told Premier it was a "huge relief" that the militants had been pushed back.
He said his friends and relatives who live there are "hugely concerned" about Boko Haram.
"The influx of refugees from Maiduguri is increasing by the day. We do not have accurate statistics now but we know that more than 50,000 have had to flee.
"I would say that about 80-90% of them are Christians because most of them that have been displaced are being taken care of by churches.
"The areas and villages that Boko Haram has attacked have been predominantly Christian areas."
Revd Canon Hassan John also urged the West to come to the aid of Nigeria as it struggles to tackle the crisis.
African leaders at a summit on Saturday offered a 7,500-strong multinational force to fight Boko Haram.
But he said this was not enough: "We do not think that the West has done enough.
"The international community does not really think that the Boko Haram campaign is...that of IS.
"There is this thinking that the Americans could have done much more if they had wanted."
Premier's Antony Bushfield speaking to Revd Canon Hassan John on Premier's News Hour: