The superhero had been declared an honorary ambassador to promote messages about women's empowerment and gender-based violence.
The character's "sexualised" appearance was one element critics seized on to deem the choice inappropriate.
A petition against the selection gathered nearly 45,000 signatures.
The UN did not explain why the project with Wonder Woman, announced in October, would end on Friday.
But spokesman Jeffrey Brez said campaigns using fictional characters often lasted no longer than a few months, Reuters news agency reported.
DC Entertainment, which publishes DC Comics, said it was pleased with the exposure Wonder Woman had brought to the cause.
Warner Bros and DC Entertainment are supporting a year-long campaign by the UN and its children's agency, Unicef, for gender equality and women's empowerment.
In the petition against the character's appointment, opponents said the image she projected was "not culturally encompassing or sensitive".
"It is alarming that the United Nations would consider using a character with an overtly sexualised image at a time when the headline news in United States and the world is the objectification of women and girls," it said.
Wonder Woman - an Amazonian from the all-female paradise of Themyscira - masquerades as Diana Prince, whose occupations include an army nurse, until her services are called on by a society in peril.
She first came to the public's attention in October 1941, and was most famously played by actress Lynda Carter in the hit US TV series that ran from 1975-79.
The announcement came as the UN itself was under criticism for having a lack of gender parity in senior roles.
Despite campaigns there has never been a female secretary general and one analysis found that in 2015 nine of 10 senior leadership jobs went to men.

A robot arm builds "babies" that get progressively better at moving without any human intervention.
The ultimate aim of the research project is to develop robots that adapt to their surroundings.
The work by teams in Cambridge and Zurich has been published in the journal PLOS One.
It seems like a plot from a science fiction film:  a robot that builds other robots  - each one better than the previous generation. But that is what researchers in Cambridge and Zurich have done.
But those concerned about machines taking over the world shouldn't worry, at least not yet.
At this stage the "baby robots" consist of plastic cubes with a motor inside. These are put together by a "mother" robot arm which glues them together in different configurations.
Although the set up is simple the system itself is ingenious.
The mother robot assesses how far its babies are able to move, and with no human intervention, improves the design so that the next one it builds can move further.
The mother robot built ten generations of children. The final version moved twice the distance of the first before its power ran out.
According to Dr Fumiya Iida of Cambridge University, who led the research with colleagues at ETH Zurich, one aim is to gain new insights into how living things evolve.
"One of the big questions in biology is how intelligence came about - we're using robotics to explore this mystery," he told BBC News.
"We think of robots as performing repetitive tasks, and they're typically designed for mass production instead of mass customisation, but we want to see robots that are capable of innovation and creativity."
Another aim is to develop robots that can improve and adapt to new situations, according to Andre Rosendo - who also worked on the project.
"You can imagine cars being built in factories and the robot looking for defects in the car and fixing them by itself," he said.
"And robots used in agriculture could try out slightly different ways of harvesting crops to see if they can improve yield."
Dr Iidya told me that he came into robotics because he was disappointed that the robots he saw in real life were not as good as the ones he saw in science fiction films such as Star Wars and Star Trek.
His aim was to change that and his approach was to draw lessons from the natural world to improve the efficiency and flexibility of traditional robotic systems.
As to whether we'd ever see robots like those in the sci-fi films that inspired him, he said: "We're not there yet, but sure, why not, maybe in about 30 years."
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The UN has ended its campaign with comic book heroine Wonder Woman, a spokesman says, less than two months after her appointment sparked outrage.
[NEXT_CONCEPT]
Engineers have developed a robotic system that can evolve and improve its performance.