Mukerji was then noted for her role in Shaad Ali's "Saathiya" (2002). Her portrayal of a medical student who struggles with married life at a young age in the film made her earn her first Filmfare Best Actress nomination and she also won her first Filmfare Critics Best Actress Award that same night. The role garnered her several Best Actress nominations at major award ceremonies, including organizations like, International Indian Film Academy (IIFA), Zee Cine and Screen which also bestowed her with a Special Jury Award. She again garnered critical acclaim and commercial success with "Chalte Chalte" (2003), "Yuva" (2004), "Hum Tum" (2004), "Veer-Zaara" (2004), "Black" (2005), "Bunty Aur Babli" (2005), "Kabhi Alvida Naa Kehna" (2006), "Laaga Chunari Mein Daag" (2007), "Saawariya" (2007), "No One Killed Jessica" (2011), "Talaash: The Answer Lies Within" (2012), "Mardaani" (2014), "Hichki" (2018) and "Mardaani 2" (2019). All these movies earned her nominations and wins at major award ceremonies, of which "Hum Tum" (2004) and "Black" (2005) won her two Filmfare Awards for Best Actress and the latter also gave her the Filmfare Critics Best Actress Award. She won Best Supporting Actress for "Yuva" (2004) and "No One Killed Jessica" (2011) respectively. She also received the Star Screen Award Jodi No. 1 for two consecutive years for her pairing opposite Abhishek Bachchan in "Bunty Aur Babli" (2005) and Shah Rukh Khan in "Kabhi Alvida Naa Kehna" (2006).