As the result of a vehicle accident in March 2012, Jagathy was hospitalized for over a year and has still not completely recovered from the injuries sustained.

The same year he played Vikram in Mammootty starrer Oru C.B.I Diary Kurippu and reprised the character in the next four sequels of the CBI Series released in 1989, 2004, 2005 and 2022 respectively.

Jagathy won the Kerala State Film Award For Second Best Actor in 1991 for his performance in the cult classic comedy movie Kilukkam and Apoorvam Chilar.

Jagathy played the role of a patient escaped from mental hospital with his group of friends in Mookilla Rajyathu (1991).

Other notable movies in the 1990s include Nagarangalil Chennu Raparkam, Cheriya Lokavum Valiya Manushyarum (1990), Kottayam Kunjachan, Koodikazhca, Kadinjool Kalyanam, Georgekutty C/O Georgekutty (1991), Ezhara Ponnana (1992), Pidakkozhi Koovunna Noottandu, Vadhu Doctoranu, Pingami, Malappuram Haji Mahanaya Joji, Kinnaripuzhayoram, CID Unnikrishnan B.A., B.Ed (1994), Oru Abhibhashakante Case Diary, Vrudhanmare Sookshikkuka, Puthukottyile Puthu Manavalan, Kusruthikaatu (1995), Kalyana Sowgandhikam, Kaathil Oru Kinnaram (1996), Arjunan Pillayum Anchu Makkalum, Kilukil Pambaram, Junior Mandrake (1997), Meenathil Thalikettu, Kottaram Veettile Apputtan, Mangalya Pallakku, Mayilpeelikkavu, Grama Panchayath, Alibabayum Arara Kallanmarum, Sreekrishnapurathe Nakshathrathilakkam (1998), Udayapuram Sulthan, Vazhunnor, Tokyo Nagarathile Viseshangal, Pattabhishekam and Friends (1999).

Jagathy's role as Krishnavilasom Bhageeratan Pilla aka Pillechan in the comedy drama Meesa Madhavan (2002) is often considered one of his career best.

[18] Jagathy won his second Kerala State Film Award for his performance in Meesa Madhavan and for doing a character role in Nizhalkuthu.

[19] Some of his memorable roles in 2003 were in movies such as Mr. Brahmachari, Thilakkam, Kilichundan Mampazham, Sadanandante Samayam, Vellithira, Swapnam Kondu Thulabharam, C.I.D.

Moosa, Meerayude Dukhavum Muthuvinte Swapnavum, Balettan, Hariharan Pillai Happy Aanu, Pulival Kalyanam and Pattanathil Sundaran.

Jagathy's next film directed by Priyadarshan after Kilichundan Mambazham, was Vettam (2004), where he played a comic serial killer called Basha.

Jagathy's other successful comedy movies in the 2000s include Vellinakshatram (2004), Naran, Kochi Rajavu (2005), Classmates (2006), The Speed Track, Chota Mumbai, Hallo, Rock & Roll (2007), Crazy Gopalan, Twenty:20 (2008), Sagar Alias Jacky Reloaded and Evidam Swargamanu (2009).

Jagathy's role as Member Ramanan in Elsamma Enna Aankutty (2010) was appreciated and the movie was a box office success.

Jagathy played the lead role in Raamanam (2009) which earned him that years Kerala State Film Special Jury Award.

Jagathy's other notable character roles are seen in movies such as Vesham (2004), Thanmathra (2005), Chess, Palunku (2006), Manchadikkuru (2008), Pazhassi Raja (2009), Indian Rupee (2011) Kerala Cafe (2009) Manikiakkallu (2011) Christian Brothers (2011) Janapriyan (2011) and 1993 Bombay, March 12 (2011).

[3] Just days before the March 2012 road accident, Jagathy had publicly revealed that he had a daughter, Sreelakshmi Sreekumar, with actress Kala, also said to be his third wife.