In the first half of her on-screen career, Manju featured in 20 films with prominent Directors and superstars producing a number of performances that earned her equal billing with the male superstars in Malayalam. She played each of these roles with consummate ease, probably the only Actress at the time who could carry a film on her shoulders. Even at school, Manju showed extra ordinary talent in dance, and won many awards. She was conferred with the Kalathilakam in Kerala Youth Festival for 2 years. She first appeared in a television serial Moharavam which was telecast on Doordarshan. At the age of 17, she debuted in the film Sakshyam (1995). Later at the age of 18, she acted in the movie Sallapam (1996), co-starring Dileep, whom she later married. Since then, she acted in around 20 Malayalam movies over a span of three years.

On 20 October 1998, Manju married actor Dileep at Aluva Sri Krishna Temple. The couple have a daughter, Meenakshi. Dileep and Manju filed for divorce in 2014 and it was granted in January 2015.

Her performance in the movie Kannezhuthi Pottum Thottu won a special mention from the jury for National Film Awards. Her other films include Kanmadam and Aaraam Thampuran with Mohanlal, Ee Puzhayum Kadannu and Kudamattam with her husband Dileep, Summer In Bethlahem, Pranayavarnangal, Pathram and Kaliyattam with Suresh Gopi, and Irattakuttikalude Achan, Kaliveedu, Thooval Kottaram and Krishnagudiyil Oru Pranayakalathu with Jayaram. She won the Kerala State Film Award for Best Actress for her performance in the movie Ee Puzhayum Kadannu. The film won three Kerala State Film Awards. In Kanmadam, she portrayed the role of a high-tempered blacksmith named Bhanu, which also starred Mohanlal. In her film Daya, Manju disguises herself as a man and does this role with full perfection. Her role as the strong-willed Devika in Pathram became popular among the audience. The film was highest grosser of the year 1999 and ran over 250 days in theatres. Her last film before she took a sabbatical was Kannezhuthi Pottum Thottu. Her portrayal as Bhadra, who takes revenge against Natesan who killed her parents, is considered her best acting performance to date. She was nominated at the National Film Awards but she lost to Shabana Azmi. She was awarded the Special Mention (acting) for her performance. In a span of four years, Manju Warrier has acted in almost 20 Malayalam films and majority of these films have been hits at the cinemas.

On October 24, 2012, she performed Kuchipudi in Guruvayur Sree Krishna Temple. Later in July 2013, she acted in a commercial with Amitabh Bachchan. Her comeback announcement was greeted with much fanfare by fans and the media. She later appeared in many advertisements for Kalyan Jewellers alongside Amitabh Bacchan, Aishwarya Rai, Akkineni Nagarjuna and Prabhu Ganesan. She recently published a book titled Sallapam.

She made her much awaited return to cinema with Rosshan Andrrews's How Old Are You in 2014. Manju played the character of Nirupama Rajeev, a UD clerk in Revenue Department. The film earned positive reviews from critics and was received well by the audiences. She received numerous accolades and became the goodwill ambassador of many ventures related to organic farming, inspired by her film .Her Next film was Sathyan Anthikad's Ennum Eppozhum which reunites her with Mohanlal after a gap of 17 years which was a moderate hit. Her next project was Rani Padmini by Aashiq Abu along with Rima Kallingal released in October 2015. The film received a negative response from the box office as it faced tight competition from other movies like Ennu Ninte Moideen and Amar Akbar Anthony.She acted in Jo and the Boy, her last release in 2015, as an Animator.Her first full-length role in 2016 was Rajesh Pillai's Vettah, a mind-game thriller, in which she appeared in the role of a police officer for the first time in her career. She acted in a Sanskrit stage drama based on Abhijñānaśākuntalam.The play was presented by Sopanam Institute of Performing Arts & Research, founded by the late Kavalam Narayana Panicker, and was hosted by Swaralaya. Manju debuted as a Producer as well and the play was produced under her banner, Manju Warrier Productions. Her next film was Karinkunnam 6S, in which she played the character of Vandana, a Volleyball coach.She also sang a song for cancer patients for the show she hosted Kerala Can(Manorama News), tuned by Ratheesh Vega, which brought in a lot of praises.

Her first release in 2017 was C/O Saira Banu, in which she appeared as a post woman. The film also marked the comeback of Amala Akkineni in Malayalam after more than two decades .Her Performance won critical acclaim and the movie was an average grosser. On September 28, her next film Udaharanam Sujatha released in Kerala. The film released to positive reviews from critics and warm response from the audience. She received huge praise for her portrayal of Sujatha, mother of a tenth class student and a person who does multiple jobs to ensure a good life for her daughter. Her next release in 2017 was Villain, an emotional thriller where she appeared as Dr. Neelima, an independent, idealistic woman and wife of Mathew Manjooran played by Mohanlal. The film went on to bag the record for the highest first day collections for a Malayalam film. The film received mixed response from critics and a positive feedback from the audience. Directors N. Lingusamy, Mysskin, Pandiraj, Thiru, and Suseenthiran were all positive about the film, particularly praising the actors' performances and the making. She of the founding members of Women in Cinema Collective, the organization for the welfare of women workers of Malayalam movie industry.