The 51-year-old was appointed by the university’s council in March after months of speculation on who would replace outgoing vice-chancellor Max Price.
The maths professor, who was born in Pretoria, went to study at the University of the North West at just 16 and obtained her PhD in 2002.
She will take the reins at UCT from July 1, and plans to ensure that the institution remains one of the best in Africa and adopts an identity that does not seek to make it something that it is not.
“If you look at the UCT’s strategic documents since the outgoing vice-chancellor came, it talks about UCT being Afropolitan and there are a lot of debates around using Afropolism rather than African,” she said.
“Being African is an identity that we should be proud of. We should not use Afropolism.
"That suggests we are a mixture of African and something else, or we are Africans somewhere in the world but not on the continent.
“That concept makes me a little uncomfortable, it denies who we are, tries to polish us, attempts to assimilate into something that is not necessarily who we are, to explain ourselves to others that we are not the poor and backward Africa they think we are.
“I’m saying we are African and we do work that can make an impact globally and is relevant to the continent, (and) that the world should sit up and take us seriously as Africans.
“I want to write something moving the institution from Afropolitan to being unapologetically African," Phakeng said.
She revealed in preparation for her new role that she met former vice-chancellors to learn from their experiences and to see how she could incorporate this into her position.
“There have been a lot of people who have come before me - Mamphela Ramphele, Professor Njabulo Ndebele, Professor Stuart Saunders, Max Price -and I’ve made an effort to meet with each of them individually because in my view there is something to be learnt from all of them,” she added.
Phakeng explained that the government’s adoption of a free higher education policy had the institution working on plans to accommodate postgraduate students whose ability to afford to continue their education should not be a hindrance.
“The big challenge for free education is not so much for universities but from the government’s side to see if they can sustain it.
"It can’t just be done for five years and (then) we are told that there is no more money.
“For us internally it's that the government is supporting us to do it for undergraduates but we don’t have it for postgraduate, so the very student who gets supported as an undergraduate, what happens to them when they want to do a postgraduate?
"Are we saying they are no longer poor, and what does that do for our transformation agenda because the majority of these students are black students?
“That is the challenge we are grappling with now, and we have started working on a model for Honours students but because it comes from institutional funding it is not available for everyone, and as we get on to our budget season in September we will (look at) how we tackle this.”
Having been faced with protests around transformation and the #RhodesMustFall campaign, Phakeng said the institution had to ensure that it tackled transformation in three phases.
“Looking at the university today, there are more black students than 15 years ago and my critique is that it's just one level of transformation.
"I always talk about three levels of transformation - access, participation and success.
"Equity of participation talks to when students are here at campus. Do they feel a part of this university and if they still feel alienated? What is the point of bringing more people here and they feel like it is not their place,” she said.
“One has to start questioning what are the things we need to transform about the institutional culture that can make sure that the people don’t feel like intruders.
“And do we have transformation at the level of success? Are we looking at who is making it, who is dropping out? And if it is black students, it should worry us and we need to ask ourselves why.
"If we are experiencing more black students who pass at a lower level or it takes them six years to complete a three-year course, it should be a challenge for us to question.
"You can say that you have succeeded at transformation at the level of access, but you have brought people here and they might be frustrated and failing here and go back worse than when they came.”
With more attacks on students on campuses being recorded across the country, Phakeng said ensuring the safety of students would need engagements with students and building trust in securing measures put in place.
“For us, that is our biggest challenge because we are an open campus, and it is not so easy to close it up and it is not something I can say I have a magic solution for.
“There is an antipathy towards security, but then we need security and it comes from our history because they don’t want to be securitised, so we are going to have to hold conversations with students around how we ensure that the campus is safe for their own protection.
"The students have to understand that we live in a society that is complex where these things happen not just at UCT but everywhere else," she said.