Rehab Abdel-Rahman has been forced to return to Egypt after losing her place at Edinburgh University's College Of Medicine And Veterinary Medicine.
She says the decision by the university authorities, which she is seeking to challenge, breaches her human rights because she has been unable to remain with her family in Scotland.
She claims a dispute with a supervisor and harassment by other academics and students halted her studies.
In the long-running dispute, the university responded by claiming that Dr Abdel-Rahman, who was previously an assistant lecturer at Ain Shams University in Cairo, Egypt, had waited too long before coming to the Court Of Session.
But judge Lord Jones has already rejected the university's attempt to have the case thrown out on procedural grounds.
The university's legal team returned to court yesterday to ask permission to appeal against the judge's decision. Their request was refused.
Dr Abdel-Rahman, who is conducting her own case, presented her arguments via a satellite television link.
"In the interests of justice the court should look into the main issues," she said.
She said the university, which accused her of dragging her feet, also bore a responsibility for delay in the marathon case.
Anna Poole, counsel for the university, said one of the reasons to appeal against Lord Jones' earlier decision was that the case should be dealt with as quickly as possible, sparing further court time and public expense.
The two sides are expected to return to court later this month to discuss further procedure.
Lord Jones heard that in August 2005 Dr Abdel-Rahman was told she could study for a PhD in genetic epidemiology and began work in September that year, expecting to gain the qualification in three years.
All appeared to be going well until October 2008 when she went on sick leave and complained to the university authorities of "severe persecution" and "harassment".
She also wrote to one of her supervisors complaining about the other supervisor.
At the time it was thought that, having completed laboratory work, her thesis could be written up and submitted within a couple of months.
During a lengthy series of exchanges after that Dr Abdel-Rahman's sick leave and suspension of her studies continued. The university offered to take her back but wanted to impose conditions that she did not accept.
Dr Abdel-Rahman was told then that her exclusion might have consequences for her visa to remain in Britain.
The university said it could not have her back because the continuing row was affecting other staff and students in the department.