The agreement was signed on Monday by Scotland's First Minister Nicola Sturgeon and Governor of California Edmund G Brown, CNBC reported.
But she also said she strongly believes it's important "to stand up and champion values that we hold dear and not allow a diplomatic silence to get in the way of doing that".
However, Mr Trump is expected to visit Scotland during his state visit, as he owns two golf resorts north of the border and his mother was born on the Isle of Lewis. But Sturgeon revoked his honorary status as a business ambassador for Scotland in 2015 after he proposed a ban on Muslims entering the United States.
Following the meeting, the First Minister said: "Scotland is making huge progress in delivering our climate change ambitions, but we are not complacent and there is still much to achieve".
She also told the audience that while she "fervently" wants Scotland to become independent, she "wouldn't want it to be won on the basis of a campaign that was as dishonest as the European Union referendum campaign".
A joint agreement committing the Scottish Government and the state of California to work together to tackle climate change has been signed.
Sturgeon said she is sure "the president has policy disagreements with me", as he will with many other governments.
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Scottish voters rejected independence in a 2014 referendum that Sturgeon's Scottish National Party called a once-in-a-generation vote.
On Wednesday, BuzzFeed News asked constitutional experts what case the Scottish government could bring forward, and they said it boils down to the wording of the Scotland Act and if it explicitly rules out Holyrood holding referendums.
Ms Sturgeon was at the United Nations building in NY last night where she gave a speech on women's rights and peacekeeping.
"This trip has been principally business focused so we're not going to Washington on this occasion", she said. She reportedly backed Democratic candidate Hillary Clinton in the election and has had no meetings with Trump or his administration during her trip, which she said has focused mainly on strengthening trade and USA investment in Scotland.
"Scotland and England should always trade freely with each other", Sturgeon said.
"That says to me there are 20 million people who are not Scottish in America but would like to be Scottish. But I want that as well as trade within the single market because that is so important to Scotland's interests".
He said: "We agree with the Prime Minister that now is not the time for a vote, but if the UK Government's intention is to try and indefinitely block a referendum that would be utterly undemocratic and unsustainable".
"However, I'm also hoping that the First Minister will return from the USA full of ideas on how to repeat the success we've had in powering our homes and businesses with renewables in order to start reducing carbon pollution from Scotland's transport and heating sectors".