Gareth Stobart said Middlesbrough Council was charging the fee for each of the 52 flats at student accommodation Linthorpe Hall 248.
He accused them of handing out "blanket" requirements, while university-owned bedrooms were exempt.
The council said it had deemed each of the flats to be "licensable dwellings".
It said because the facility is "privately owned and operated", it was no different to hundreds of other privately-rented properties where the fee must be paid.
The fee, introduced as part of a five-year scheme to "improve" standards of private rentals, is charged per home or property inselected Middlesbrough areas.
However Mr Stobart, group property manager at Linthorpe Property Management, said he and other landlords were being put in the "firing line" when charged per flat.
"It's just crazy," he told theLocal Democracy Reporting Service.
His company charges up to Â£100 per week for an en suite room and access to shared facilities such as kitchens, according to its website.
Mr Stobart the company was still dealing with the impact of Covid and far fewer students moving to the town as a result.
Meanwhile, he said the building had been designated as purpose-built student accommodation but he had been told it would be classified as houses of multiple occupation (HMO) for the purposes of the fee.
"No other student properties of our size are required to pay a licence [because] the council states they are operated by an educational body so don't require one," he said.
"Why aren't the university-operated buildings being classed as HMOs?"
The licence, which applies in the town's Newport area and is meant to provide support and advice for landlords, was introduced in 2019 but is due to be reviewed in a few months.
Some landlords have questioned its effectiveness and said they werestill being charged the full rate, despite the scheme potentially coming to an end next year.
They also suggested that the cost was being passed to their tenants.
A council spokesperson maintained that Linthorpe Hall 248 was not exempt as it is not controlled by an "educational establishment".
It said the scheme, which is known as "selective licensing" and was established to improve housing conditions, was approved following a three-month consultation.
"The income generated by the licence fee pays solely for the staff who deliver the scheme and the council makes no profit," they added.
A council that introduced a yearly fee of more than Â£800 for landlords has defended a decision to charge an owner in Middlesbrough about Â£43,000.