In early December, MacGowan, 65, was admitted to hospital due to an infection.
His wife Victoria Mary Clarke later announced that the singer had been diagnosed with encephalitis, an uncommon condition that causes the brain to swell and can be life-threatening.
Those with serious cases can be left with problems such as seizures, hearing loss, and blindness.
Hours before midnight on New Year’s Eve (31 December), the “Fairytale of New York” musician gave fans an update on his condition.
“Hi friends, I’m sitting here suffering from encephalitis,”said MacGowan in a video. He was wearing sunglasses and a cross necklace in the clip.
“The light is killing me,” he said, explaining his choice of eyewear. “But I wanted to wish you a Happy New Year and Happy Christmas and many more.
“All the luck in the world and all the love. Happy Christmas and Happy New Year, love Shane.”
He captioned the clip: “Happy New Year. Have as much fun as you can when you can!!! Thank you.”
Reflecting on when MacGowan became ill on 5 December, Clarke told The Sunday Independent: “I noticed it on his face. His eye was getting red and began to close over. I called the doctor and the doctor said it was very dangerous so we had to get him to the hospital straight away.
“The hospital explained to me that shingles can go into your brain and that’s what happened to Shane so now they want to keep him on a drip for two weeks.”
Clarke, 56, said that MacGowan appears “perfectly normal now” but “p***ed he can’t drink in the hospital”.
MacGowan turned 65 on Christmas Day (25 December).