Pao took over earlier this year as Reddit CEO after being fired from the prominent venture capital firm Kleiner Perkins Caufield and Byers, prompting a highly publicised lawsuit.
But she quickly ruffled feathers and provoked anger with the unexplained firing of a Reddit employee, leading to an online petition calling for her departure.
Reddit, which has more than 163 million users and describes itself as a forum for real-time journalism, said in a statement that Pao resigned "by mutual agreement" and would be replaced by founder and original CEO Steve Huffman.
"We are thankful for Ellen's many contributions to Reddit and the technology industry generally," the statement said.
"She brought focus to chaos, recruited a world-class team of executives and drove growth. She brought a face to Reddit that changed perceptions, and is a pioneer for women in the tech industry. She will remain as an adviser to the board through the end of 2015."
A California jury rejected Pao's charges of gender discrimination against KPCB in a closely-watched case seen by some as a proxy trial of Silicon Valley sex bias.
The state court jury found KPCB did not discriminate against Pao, who claimed she was fired after complaining about bias at the firm that notably backed Amazon, Facebook and Google.
Pao has said she will appeal.
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