He has been in charge of America's largest school system for 21 months and was appointed as an outside candidate following the stormy tenure of his predecessor, Joseph Fernandez.
It was hoped back in 1993 that he could bring peace and quiet to a system which had been fighting over issues like putting condoms in schools.
In the event he became mired in battles with Mayor Rudolph Giuliani who belittled him personally and professionally and repeatedly started investigations into his conduct.
In so doing, the Mayor said he wanted to get more control over the schools.
The last straw for Cortines came last month, when the Mayor decided to set up a commission to investigate the school system's handling of safety and violence. "I think you come to a particular time where you know that you can't do any more. I've taken it as far as I can go," said Cortines.
This is not the first time that Mr Cortines has said he was resigning. But this time he seems to mean it.
In April last year, after a budget dispute with City Hall in which the Mayor accused him of dragging his feet on cutting the school bureaucracy, Mr Cortines said he was quitting. But, within days, he had patched up his feud with the Mayor and rescinded his resignation.
Violence in schools became the latest battleground when Mayor Giuliani demanded that Mr Cortines hand over school security to the police department which is controlled by the Mayor. Mr Cortines resisted.
Then, without consulting Mr Cortines or the school board, the Mayor announced the school safety commission. Its five members either work for Mr Giuliani or have done so in the past. Mr Cortines complained it was a panel of "cronies" and that its report was a foregone conclusion.
One of the problems with a school district like New York is that it is run as a large and cumbersome bureaucracy. Schools have relatively little autonomy and all the responsiblity falls on the shoulders of the chancellor, who is required to be super-human.
Some observers are calling for a new system, one in which autonomy is pushed down to the schools, as has happened in a city like Chicago.
The bureaucracy creates inefficiency and corruption. One recent example was contained in a report on school food in New York which showed officials had covered up outbreaks of food poisoning and approved huge shipments of rancid beef, chicken and turkey to school cafeterias.
Chancellor Cortines had to remove the top three food service officials.
The report showed that the organisation was completely out of control. Food was often stored for months, and sometimes, years, longer than it should have been.
Mayor Giuliani used this investigation to take another gibe at the school system. It was he said: "Another indication of how the Board of Education is out of control".