1993–97: Critical and commercial success

In 1993, Khan garnered appreciation for portraying negative roles, that of an obsessive lover and a murderer, respectively, in the box office hits, Darr and Baazigar. The "Encyclopedia of Hindi Cinema" analyzed that "he defied the image of the conventional hero in both these films and created his own version of the revisionist hero." Darr marked the first of many collaborations of Khan with film-maker Yash Chopra and his banner Yash Raj Films. Khan's stammering in the film and the usage of the phrase, "I love you, Kkkiran," were popular with the audiences. His other release, Baazigar, in which he played an ambiguous avenger who murders his girlfriend, "shocked the Indian audiences" with an unexpected violation of the standard Bollywood formula. His performance in Baazigar won him his first Filmfare Best Actor Award.
The same year, Khan played the role of a love-struck musician in Kundan Shah's dramedy Kabhi Haan Kabhi Naa, a performance that earned him a Filmfare Critics Award for Best Performance. In a retrospective review by Rediff, Sukanya Verma called it Khan's best performance and added, "He was spontaneous, vulnerable, boyish, mischievous and acting straight from the heart." Khan, himself, considers this film to the best film that he has acted in. In 1994, Khan once again played an obsessive lover in Anjaam, co-starring Madhuri Dixit. Though the film was a commercial failiure, Khan's performance earned him the Filmfare Best Villain Award.

In 1995, Khan starred in two box-office blockbusters. His first release was Rakesh Roshan's melodramatic thriller Karan Arjun, in which Khan was a part of an ensemble cast that included Salman Khan, Kajol, Mamta Kulkarni, Raakhee and Amrish Puri. The film, which dealt with the concept of reincarnation, became the second-highest grossing film of the year in India. He followed it with Aditya Chopra's directorial debut, the romance Dilwale Dulhania Le Jayenge. A major critical and commercial success, the film became the year's top-grossing production in India and abroad. The film was declared an "all time blockbuster"; it remains the longest-running film in the history of Indian cinema and as of 2011, it is still playing at the Maratha Mandir theatre in Mumbai. Dilwale Dulhania Le Jayenge has grossed over 1.2 billion worldwide. The film won ten Filmfare Awards, and Khan's performance as a young NRI who falls for Kajol's character while on a trip across Europe won him critical acclaim and his second Best Actor Award at the Filmfare. In 2005, Indiatimes Movies ranked the film amongst the 25 Must See Bollywood Films, citing it as a "trendsetter of sorts". Raja Sen reviewed, "Khan gives a fabulous performance, redefining the lover for the 1990s with great panache. He's cool and flippant, but sincere enough to appeal to the junta [audience]. The performance itself is, like the best in the business, played well enough to come across as effortless, as non-acting. "
1996 proved to be a disappointing year for Khan, as he appeared in two critical and commercial failiures, Praveen Nischol's English Babu Desi Mem and Mahesh Bhatt' Chaahat However, in 1997, his starring role in Subhash Ghai's social drama Pardes earned him commercial success. The film, which also featured Mahima Chaudhry and Apurva Agnihotri, saw him portray the role of Arjun, a musician facing a moral dilemma. His performance earned him a nomination for the Best Actor at the Filmfare Award ceremony. He then featured in Aziz Mirza's romantic comedy, Yes Boss, opposite Juhi Chawla. Upon release, the film performed moderately well at the box-office. His final release of the year was Yash Chopra's blockbuster musical romanance, Dil to Pagal Hai. The project, also featuring Madhuri Dixit and Karishma Kapoor, marked his second collaboration with the filmmaker. Khan essayed the role of Rahul, a stage director who falls in love with one of his new actresses, played by Dixit. The film as well as his performance met with critical appreciation; he won his third Best Actor Award at the Filmfare.