The Rhodes University Council - the institution's highest decision-making body - has decided it was not a "prudent" time to rename the university.
Over the past few years the university has faced a growing outcry from student activists and Fees Must Fall leaders over its name, with many students referring to it as the "university currently known as Rhodes".
In a statement, the university said its council initiated a process to advance transformation and address some of the concerns raised by students in 2015 - the name being one of the main considerations.
The council met on November 30 and discussed the topic, along with a range of other issues.
However, the university decided not to change its name at this stage.
"Council deliberated extensively about the many aspects and possible consequences of the decision under consideration. Council members accepted that, when it comes to the issue of the name of the university, it could not reconcile some of the differences and it was unlikely to emerge with a decision immunised from significant consequences," the university said in a statement on Wednesday.
A path to reimagine itself
The university said it had been pursuing a path to reimagine itself as part of its transformation drive. However, this would be incomplete as long as the university still shared a name with Cecil John Rhodes.
"It would not be prudent to rename the university and invest significant financial and other resources in a major international rebranding project with limited, if any, guarantee that the identity and reputation that have drawn learners and leading scholars from South Africa, the African continent and across the globe to our university would, at the very least, remain recognisable," it said.
The university said it had recently obtained permission from the families of struggle stalwarts Charlotte Maxeke and Robert Sobukwe, and Enoch Sontonga - who composed Nkosi Sikelel' iAfrika - to use their names to rename some buildings.
"Rhodes University has been, and remains, committed to the redress of the wrongs of the past and to build an even stronger institution that every African, including all the residents of Makana local municipality, can be proud of," the university said.
Some of the other main concerns that the university said should be considered before changing the name was grappling with the university's financial sustainability, staff remuneration, employment equity, and Student Financial Aid.
"There are many academically-capable young people who, through no fault of their own, cannot afford to access a quality higher education. Every year our university invests about R38m to assist academically-deserving students who are in financial need," the university said.
Other issues include the upliftment of the local community, maintaining infrastructure, and addressing institutional culture.