Apologetic organisation Ravi Zacharias International Ministries (RVIM), which Qureshi was a part of, confirmed the news on Saturday.
Qureshi was 34 and left behind a wife and a two-year-old daughter.
RVIM said in a statement: "We know this is Nabeel's gain, but a tremendous loss for all those who loved him and were impacted by his life and testimony on earth."
David Wood, an American evangelical missionary who led Qureshi to Christ, has paid his respects to his close friend online.
Qureshi converted to Christianity from Islam after engaging in discussions with Christians while at university.
He's written several books about the two religions. The book, Seeking Allah, Finding Jesus, was a New York Times bestseller.
During his health battle Qureshi posted a series of video blogs to Youtube, some from his hospital bed.
Qureshi announced the news of his declining health in August 2016.
In the announcement he said he "never expect to make" he called his diagnosis "quite grim" but asked for prayers and still believed God for healing.
He had to cancel almost all speaking engagements and step back from his work with RVIM.