The 65-year-old woman, named as Rasmiya Awad, was detained on Monday alongside several family members near the Syrian town of Azaz, which is controlled by Turkish-backed forces in the region, Efe news reported.
"The arrest of Baghdadi's sister is yet another example of the success of our counter-terrorism operations," Fahrettin Altun, Communications Director of the Turkish Presidency, said in a tweet on Tuesday morning.
"Turkey's struggle against terror, independent of its ideology and roots, is ongoing with all its strength."
Five children, her husband and daughter-in-law were also detained and would be interrogated, according to reports.
The Istanbul-based Daily Hurriyet newspaper cited a Turkish security official saying: "We hope to gather a trove of intelligence from Baghdadi's sister on the inner workings of IS."
But experts have said that it was not clear how much useful intelligence Awad could provide, or how much time she spent with Baghdadi.
"I don't think she'd be privy to any imminent attack plans, but she might know smuggling routes. She might know networks that Baghdadi trusted, people that he trusted, networks in Iraq that helped her facilitate her own travel and her family's travel," Mike Pregent, a counter terrorism expert at the Washington-based think-tank, Hudson Institute told BBC News.
"This should be able to give our US intelligence and other allied intelligence officers a view into (IS) networks and how they moved family members, how they travelled and who they trusted."
US President Donald Trump announced the death of Baghdadi at a press conference at the White House on October 27.
According to Trump, Baghdadi detonated his suicide vest after fleeing into a tunnel during a US raid on his hideout in Syria's Idlib province.
Trump said DNA tests were carried out to verify Baghdadi's identity, confirming his death.
After the raid, the compound was destroyed in an air strike.
Abu Ibrahim al-Hashemi al-Qurashi has since been named as IS's new leader and "caliph".
( With inputs from IANS )