Muhammad Junaid was born on 8 October 1953, in the village of Babunagar in Fatikchhari Thana, Chittagong District, East Bengal, Pakistan (now Bangladesh).

His father, Muhammad Abul Hasan, was a scholar of Quranic exegesis and senior professor at Al-Jamiatul Ahlia Darul Ulum Moinul Islam in Hathazari.

[5] At the age of five, he entered Al-Jamiatul Islamiah Azizul Uloom Babunagar where he completed his hifz and basic Islamic and primary studies.

His thesis was titled Sīrah al-Imām ad-Dārimī wa at-Tarīkh bi-Shaykhihī (Biography of Imam Darimi and the history of his teachers) in 1978.

[7][8] On 15 November 2020, Babunagari was elected the new Amir of Hefajat-e-Islam Bangladesh, replacing the group's founder, Shah Ahmad Shafi, who had died two month earlier.

[6][9] On 11 April 2021, during a press conference, Babunagari claimed that COVID-19 would not spread in madrasas and demanded that these institutions be allowed to remain open during the lockdown.