Panchakarma therapy is the Actual strength of Ayurveda, which includes Five Karmas (Procedures) viz. Vamana, Virechana, Basti (Asthapana & Anuvasana), Raktamokshana. Department is having different compartments for different Karmas. These include Poorvakarma (Pre-procedures) like Snehana (Oleation & Massage) Kaksha, Swedana (Fomentation/Steam bath) Kaksha. Nasya (Nasal administration of Medicine) Kaksha and Raktamokshana (Blood Letting) Kaksha. Other Procedures like Shirodhara, Shirobasti, Shiropichu and Shiro-Abhyanga are to be conducted on Shirodhara table. 

A special Netra Tarpana procedure is also done for Ophthalmic Problems. Jalouka (Leech) are preserved in Mud pot and are used for Raktamokshana (Leech therapy) purpose. Agni karma (Cauterization) is mainly done in separate compartment which is useful for Vata-vikaras. Special procedures like Janu-Basti, Kati-Basti, Manya-Basti, and Hrudh-Basti are also performed. Pinda Sweda is done routinely with other special Keralian Panchakarma procedures like Pizhichil in this department.

Kayachikitsa and Panchakarma department has undertaken a project-A paralysis care centre. Many patients are benefited through this project. Snehana, Pindasweda, Shirodhara, Raktamokshana, Basti therapy are done in this centre.

Various camps are also arranger throught the year. Vasantik Vaman camp in Vasant Rutu, Virechana camp in Sharad Rutu, Basti camp in Varsha Rutu is the most important among those camps.