Sheikh Hasina, who has ruled since 2009, had defied weeks of demands for her to stand down.
Bangladesh Prime Minister Sheikh Hasina resigned today and left the country following more than a month of deadly anti-government protests. Army chief General Waker-Us-Zaman said that an interim government would be formed.
The 76-year-old leader is said to have flown in a Bangladesh military aircraft with her sister, reports said.
Footage from airline tracker Flight Radar showed an aircraft of Bangladesh Air Force - Lockheed C-130J Hercules - flying over India. The plane was seen flying over Jharkhand.
Earlier, some reports claimed that Ms Hasina would fly to West Bengal but as per the airline data, the aircraft bypassed the state.
Ms Hasina, who has ruled since 2009, had defied weeks of demands for her to stand down but fled following a brutal day of unrest on Sunday in which nearly 100 people died.
As per sources, her security team asked her to leave and that she did not find any time to prepare.
The country witnessed chaotic scenes from this morning that culminated in Ms Hasina's resignation. Huge crowds were seen waving flags, and dancing on top of a tank in the streets before hundreds broke through the gates of Ms Hasina'a official residence.
Some smashed a statue of her father Sheikh Mujibur Rahman, the country's independence hero.
Earlier, Ms Hasina's son urged the security forces to block any takeover from her 15-year-rule.
"Your duty is to keep our people safe and our country safe and to uphold the constitution," her son, US-based Sajeeb Wazed Joy, said in a post on Facebook.
"It means don't allow any unelected government to come in power for one minute, it is your duty."
The country's military and other security forces had supported Ms Hasina's government through the unrest that began last month against civil services jobs. The protests escalated into wider calls for her to stand down.
The demonstrations were about the reintroduction pf a quota scheme that reserved more than half of all government jobs for certain groups.
Ms Hasina won her fourth consecutive election in January in an election without a genuine opposition.