Last week, Mr Pence said the US should be prepared to bomb Syrian military targets to protect civilians in the besieged city of Aleppo.
When asked about Mr Pence's position during the second presidential debate, Mr Trump said: "He and I haven't spoken, and I disagree.
"I believe we have to get Isis," the Republican presidential nominee continued. "We have to worry about Isis, before we can get too much more involved" in Syria.
In pictures: Russian air strikes in Syria
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He went on to say: "I don't like Assad at all. But Assad is killing Isis, Russia is killing Isis, and Iran is killing Isis."
While Mr Trump didn't explicitly give his support to the Syrian regime, his comments suggest he supports the status quo.
Activists from Raqqa is Being Slaughtered Silently (RBSS) published a series of tweets fact checking Mr Trump's statements and accusing him of being a liar.
Syrian President Bashar al-Assad's government has mostly focused on combating Syrian opposition groups, some of which are supported by the US.
Similarly, while Russia asserts it is fighting Isis extremists in Syria, the majority of its air strikes have targeted opposition groups threatening the Syrian regime.
The fight against Isis is predominantly being waged by a US-led coalition, with help from Turkey, by training, advising and equipping Syrian Arab and Kurdish fighters.
The Assad regime has been accused of killing more civilians than Isis and has been severely criticised for indiscriminately using barrel bombs on civilian areas.
Investigators found the Syrian government responsible for "massive and systematised violence" and said the crimes against humanity committed by the regime far outnumber committed by Isis and other jihadist groups.
When asked what he thinks would happen if Aleppo falls, Mr Trump said the besieged city "basically has fallen".
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