The protest took place when the Pakistani cricketer- turned-politician along with his new wife Reham Khan arrived at the Army Public School to meet the students.
The parents of deceased students who lost their children in the school tragedy chanted "Go Imran Go" while holding placards rejecting Khan's visit.
The attack claimed lives of 150 people, including 134 children, who were butchered by Taliban militants. The school reopened on Monday after remaining closed for weeks.
The parents were also angry with Khan for politicising the attack. "Do not pour in politics all over the blood of our children," said an angry parent.
Several leaders of Pakistan Tehreek-e-Insaf (PTI) party also accompained Khan during his visit to the school.
The relatives said that he was busy with his marriage when the people of the city suffered, a reference to his recent marriage with TV anchor Reham.
Parents, including others, cried and heaped scorn at the PTI leader and his fellow politicians including chief minister Pervez Khattak.
One of the protesters climbed on the vehicle of Khattak. Other chanted slogan and raised placards.
"You were busy getting married without doing anything about my child who died less than a month ago," said a weeping mother.
"Imran came after one month to visit the school because he was busy with his wedding," said another angry parent.
The crowd also scuffled with the police but did not let Khan and his wife enter by the main gate.
They were later ushered through a back gate to meet the children.
Khan's party has been ruling the province since 2013 after election but so far has failed to deal with the issue of law and order.
On January 12, Khan had tweeted that he along with his wife and Khyber Pakhtunkhwa Chief Minister were going to visit the school on the opening of the school following the attack. Imran tweeted that he was advised to postpone the visit as the Chief of the Army Staff would be visiting the school.