Ousted: Mahbod Moghadam, left, co-founder of Rap Genius. Photo: Getty Images
Moghadam wrote a series of annotations on a version of Rodger's manifesto uploaded to Rap Genius, stating that parts were "beautifully written" and saying that he guessed Rodger's sister was "smoking hot".
The company announced the departure in a blog post on its website.
One of the comments posted by Mahbod Moghadam.
"In light of this, Mahbod has resigned – both in his capacity as an employee of the company, and as a member of our board of directors, effective immediately," wrote Tom Lehman, co-founder and chief executive of Rap Genius.
Technology news website Re/Code reported that Moghadam was fired after pressure from the company's investors.
TechCrunch reported that it wasn't the first time Moghadam had said something controversial.
In an interview, Moghadam reportedly told start-up newsletter WakeField that Facebook founder Mark Zuckerberg could "suck my d--k".
Moghadam made the comment after Zuckerberg requested a photo Moghadam posted to Instagram of Zuckerberg, rapper Nas and investor Ben Horowitz be taken down.
Moghadam later blamed the outburst on a brain tumour he unknowingly had growing inside him, which he said was making him mean.
Moghadam posted an apology to Twitter on Monday, although he did not specify the exact reason for it.
"I want to apologise to everyone," he tweeted. "I need to hear these criticisms, reflect for real, and work on becoming a better person."
I want to apologize to everyone. I need to hear these criticisms, reflect for real, and work on becoming a better person — Mabode (@mahbodmoghadam) May 26, 2014
Moghadam also released a statement to Valleywag after his comments received widespread attention.
"I was fascinated by the fact that a text was associated with such a heartbreaking crime, especially since Elliot is talking about my neighbourhood growing up," he said.
"I got carried away with making the annotations and making any comment about his sister was in horrible taste, thankfully the Rap Genius community edits out my poor judgement, I am very sorry for writing it."
Rap Genius did not immediately respond to a request for comment.
The New York-based company, which was formed in 2009 by two Yale graduates, has attracted $US15 million in investment to date.
Fairfax Media, Mashable