Owner Mike McLeod went from fighting a multi-national company to keep the name when he purchased the venue, to being "very happy" to remove his association with it.
The name received flack in the wake of Black Lives Matter marches and a global movement to remove public statues as a protest against systematic racism.
- Protesters target two statues of historic figures
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Mr McLeod wanted to have a conversation with the public about the name, and said he spend a few days getting feedback.
Despite being met with a mixed response, only one response was backed up with good reason, he said.
"I had quite a lot of people telling me not to change the name, but when I started looking at the reasons that people were giving ... I realised most of the people who wanted me to keep the name were just saying, it had always been that."
He said that was not a good enough reason.
"I am comfortable with the decision to remove it."
In a post on the venue’s Facebook page, he outlined his reasoning for the name change, saying Captain Cook was a symbol of colonisation and oppression.
"Because people are hurting, and I did not do this to ostracise and hurt people, I did not want to remind people of oppression and suffering when they came to the venue."
Mr McLeod said he received some backlash over his decision to change the name from people saying they would no longer come to the venue, but it had not concerned him.
The majority of the negative feedback had been directed to his old restaurant page, which led him to believe they were from people who had never come to his new music venue, or realised the downstairs had become a pizza restaurant.
Mr McLeod said he had a few name ideas, and may speak to local iwi about the possibility of using a Maori name, with the hope of having a new name within a week.
Mr McLeod said in the post people had suggested he change the name when he first took over the business.
"I'm no hero for taking two years to understand what they were saying."
The Captain Cook Hotel opened in 1860, and later became a well-known music venue and watering hole for the city’s university students.
It closed in 2013 but reopened in 2018 under operator Mr McLeod.
Last year, the gastro-pub venture on the ground floor closed when New Zealand-based pizza franchise company Sal's took over the lease.
Mr McLeod continues to operate the live music venue upstairs.
