The incident involving the 10:13 service happened close to Inverurie.
ScotRail Alliance said no-one was injured in the collision, but that the damage included a smashed windscreen and engine failure.
Services between Aberdeen, Inverurie and Inverness were affected until early afternoon.
A ScotRail Alliance spokesperson said: "Due to a train hitting a tree between Aberdeen and Inverness services along the route are disrupted.
"We have replacement buses in place to get our customers where they need to be.
"We apologise to anyone delayed by this incident."

Sheikh Nawwaf al-Melhem, a leader of the officially-tolerated opposition People's Party, told the BBC he had brokered an agreement between the state and inmates at Hama Central Prison.
The prison's power and water supplies had now been restored, he said.
Interior Minister Mohammed Shaar said the situation at the prison was normal and denied there had been any disorder.
Human rights and opposition activists say the prisoners took guards hostage about a week ago as they tried to halt the transfer of several inmates to another facility where they believed they might be executed.
Security forces reportedly surrounded the jail and twice failed to retake it by force.
Sheikh Nawwaf, who is also a prominent tribal leader in central Syria, said he travelled to Hama Prison on Saturday afternoon.
The inmates' demands focused on ensuring fair and speedy trials for those detained without trial, and the release of those held without charge, he added.
Sheikh Nawwaf said he had presented the demands to Mr Shaar and Justice Minister Najm Hamad al-Ahmed in Hama on Sunday.
He said a deal to end the mutiny was reached later that day and included a promise from the government of fair trials for political detainees.
Leading rights activist Mazen Darwish, who is in touch with the prisoners, confirmed that a verbal agreement had been reached, but did not give any details.
Another activist told Reuters news agency the government had "agreed to most of our demands to release those political detainees held without charge".
The Syrian Observatory for Human Rights, a UK-based group that monitors the conflict in Syria, reported that 26 detainees would be released soon.
Later on Monday, the official Sana news agency reported that Mr Shaar and Mr Ahmed had visited the prison, and that they promised to "provide inmates' needs" and ensure that none were mistreated.
But it also cited a statement by the interior minister as saying that the situation there was "normal, contrary to the lies and fabrications spread by malicious media outlets as part of their anti-Syria propaganda".
The reported deal came after conditions worsened inside the prison, with authorities cutting electricity and water supplies, and inmates reporting a food shortage and serious medical cases.
Security forces also tried to storm the cell block where the prisoners were holding out on Friday and Saturday, using tear gas, rubber bullets and live ammunition.
The BBC was told that 15 prisoners were shot and wounded.
The revolt was sparked by a move to transfer several detainees to the notorious Sednaya Prison near Damascus.
"You can't imagine, even in your worst nightmare, what kind of torture [takes place] in Sednaya," a lawyer who is in contact with the prisoners told the BBC.
One activist group, the Syrian Network for Human Rights, has documented the arrest and detention of more than 117,000 people in Syria since the uprising against President Bashar al-Assad began in March 2011.

Charlie ran on to the pitch during New Zealand's lap of honour at Twickenham stadium last night.
Sonny Bill Williams intervened as a security guard tackled the 14-year-old fan.
The New Zealand centre took Charlie with him on his lap of honour before giving him a surprise he will not forget.
Williams handed over his Rugby World Cup winners medal in front of a stunned crowd.
He told New Zealand News afterwards: "I was walking around doing a lap of honour with the boys and a young fella came running out and he got smoked by the security guard, like full-on tackled him. I felt sorry for the little fella."
It's a Rugby World Cup final souvenir that Charlie wont forget.
Rail service have been disrupted after an Aberdeen to Inverness train was damaged when it hit a fallen tree in Aberdeenshire.
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A deal is reported to have been reached to end a mutiny at a prison in Syria by hundreds of mostly political detainees.
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New Zealand player, Sonny Bill Williams, gives his Rugby World Cup winning medal to a stunned 14-year-old fan.