A gay man who has been living in Brisbane for four years will be deported next week after his application for a partnership visa was refused.

This will put him at risk of being jailed in the country of his birth for being openly homosexual.

Ali Choudhry grew up in the United States and has few contacts in Pakistan.

He cannot read or write the local language.

He has been in a relationship with Brisbane neuroscientist Dr Matthew Hynd for the past four years.

Mr Choudhry and Dr Hynd were one of the first gay couples in Queensland to register their civil union on March 12, 2012.

It was a significant day that they celebrated with family and friends.

Nearly two years later, Mr Choudhry's application for a visa recognising his relationship with Dr Hynd has been refused.

He says he cannot understand why theirs is not considered a legitimate long-term partnership.

"We applied for a partnership visa to try and keep me here, and keep us together," he said.

"For us, for whatever reason, it took about two years, and then even after all that time, it came back as a no."

Fears imprisonment in Pakistan

Mr Choudhry faces harassment and possible life imprisonment in Pakistan for being gay.

Dr Hynd says they do not know what to do.

"The worst case is, Ali will be deported next week on his birthday," he said.

"You know, what do we do now? To go back to a country where, you know, there is life imprisonment for being gay.

"And, I mean, he grew up in America, he's never lived in Pakistan.

"By country of birth, yes, but this is a country where he doesn't read the language - he can speak it - but how are you supposed to then get a job?"

Survived floods to set up business

Mr Choudhry lost all his possessions in the Brisbane floods.

He has since set up a photography business in Brisbane, but is preparing for deportation on January 8.

"Marriage equality and things like that are things that really do need to happen and happen soon, sooner than later," Mr Choudhry said.

Two weeks ago, he was notified that he must leave Australia after his visa review application to Immigration Minister Scott Morrison was also rejected.

Mr Choudhry has now lodged an appeal to the Migration Review Tribunal.

Mr Morrison was not available for interview.

His spokesman said in a statement that same-sex couples are assessed no differently from heterosexual couples regarding immigration matters.

The spokesman said while they cannot comment on individual cases for privacy reasons, all applicants must meet relevant criteria to be granted a visa and that these extend beyond whether there is a genuine and ongoing relationship.

Dr Hynd says the ramifications of the visa rejection for both of them are dire.

"We have no idea what else we can do other than invite maybe the Immigration Minister into our bed and say, hey, this is two guys sleeping in the same bed.

"If you do not believe that, you know, we're in a relationship, then I just don't know."