"It's been a rough couple years," adding that he was also suffering from a chronic viral infection.
The star said he was aware of social media speculation that he had a drug problem, after he was pictured looking unwell with blotches on his skin.
Lyme disease is caused by bacteria carried by some species of ticks.
Symptoms of the infection often include a rash, muscle pain, and tiredness.
On his Instagram page, the artist wrote that people had suggested he looked like he was "on meth", but "they failed to realise I've been recently diagnosed with Lyme disease, not only that but had a serious case of chronic mono which affected my skin, brain function, energy, and overall health".
He said he was getting "the right treatment" to help address the disease, and that more would be revealed in an upcoming YouTube documentary series about his life.
"You can learn all that I've been battling and OVERCOMING!!" he wrote, telling his 124 million Instagram followers: "I will be back and better than ever".
The superstar's wife, model Hailey Bieber, defended her husband against criticism from those "trying to downplay the severity of Lyme disease"."Please do your research," she urged them on Twitter on Wednesday.