Haley, who has criticized the president on some foreign policy points, wrote a column in September denying that she penned an explosive New York Times op-ed. In the Times piece, an anonymous "senior administration official" said people working for Trump have worked to undermine his worst impulses on issues such as trade and Russia policy.
"I, too, am a senior Trump administration official. I proudly serve in this administration, and I enthusiastically support most of its decisions and the direction it is taking the country," Haley wrote. "But I don't agree with the president on everything. When there is disagreement, there is a right way and a wrong way to address it. I pick up the phone and call him or meet with him in person."
Haley had her critics in the White House, and she scrapped back, as well. Top economic advisor Larry Kudlow had suggested she suffered from confusion earlier this year when she said new sanctions against Russia were coming. Haley responded by saying, "With all due respect, I don't get confused." Kudlow, in turn, apologized. But the incident apparently left a mark.
Ethics groups recently requested an investigation into Haley over whether she inappropriately accepted flights from South Carolina businessmen. It was unclear if those ethics concerns related at all to her departure, and the White House did not comment on her reason for leaving.
Read Haley's full resignation letter to Trump below:
October 3, 2018
Dear Mr. President:
It has been an immense honor to serve our country in your Administration. I cannot thank you enough for giving me this opportunity.
You will recall that when you offered me the position of United States Ambassador to the United Nations in November 2016, I accepted the offer based on some conditions. Those conditions included serving in your Cabinet and on the National Security Council and being free to speak my mind on the issues of the day. You made those commitments and you have absolutely kept them all. For that too, I will always be grateful.
We achieved great successes at the UN. We passed the toughest sanctions against any country in a generation, pressuring North Korea toward denuclearization. We passed an arms embargo on South Sudan that will help reduce violence and hopefully bring peace to that troubled country. We stood up for our ally Israel and began to roll back the UN's relentless bias against her. We reformed UN operations and saved over $1.3 billion. We spoke out resolutely against dictatorships in Iran, Syria, Venezuela, Cuba, and yes, Russia. Through it all, we stood strong for American values and interests, always placing America first. I am proud of our record.
As a strong supporter of term limits, I have long believed that rotation in office benefits the public. Between the UN Ambassadorship and serving in the South Carolina Governorship and General Assembly, I have been in public office for fourteen straight years. As a businessman, I expect you will appreciate my sense that returning from government to the private sector is not a step down but a step up.
Accordingly, I am resigning my position. To give you time to select a replacement, and to give the Senate time to consider your selection, I am prepared to continue to serve until January 2019.
At that point, I will once again become a private citizen. I expect to continue to speak out from time to time on important public policy matters, but I will surely not be a candidate for any office in 2020. As a private citizen, I look forward to supporting your re-election as President, and supporting the policies that will continue to move our great country toward even greater heights.
With best wishes and deep gratitude,
-CNBC's Eamon Javers contributed to this report.