BackgroundPost-COVID-19 syndrome is a result of triggering various immune pathways and metabolic disturbances.Bastiis an important per rectal Ayurveda-based treatment having multi-targeted actions.BastiandRasayanatreatment modulate immune responses by regulating pro-inflammatory cytokines, immune globulins, and functional properties of T cell. We propose to study the clinical evaluation ofBastialong withRasayana(rejuvenation therapy) on symptoms of post-COVID 19 syndrome.Methods and analysisWe designed a prospective, open-labeled proof of concept pragmatic study. The study duration is 18 months, and the intervention period are 35 days from the day of enrollment of the patients. The patients will be treated on the basis of Ayurvedic classification ofSantarpanottha(over nutrition) symptoms andApatarpanottha (lack of nutrition)symptoms. TheSantarpanotthagroup will be treated within 3–5 days of oralGuggulu Tiktak Kashayamfollowed by 8 days ofYog Bastitreatment and then 21 days ofRasayanatherapy withBrahma Rasayan. TheApatarpanotthagroup will be treated within 3–5 days of oralLaghumalini Vasant, followed by 8 days ofYog Bastitreatment and then 21 days ofKalyanak Ghrit.The outcome measures of this study will be to evaluate the changes in fatigue severity scale, MMRC dyspnea chest pain scale, pain score assessed by VAS scale, smell and taste scale, WOMAC scale, Hamilton depression scale, Hamilton anxiety scale, Insomnia Severity Index, change in Cough Severity Index, facial aging scale, dizziness scale, Pittsburgh Sleep Severity Quality Index, functional status scale, and heart palpitation scale.All adverse events will be monitored at each time throughout the study visit time. A total of 24 participants will be recruited to demonstrate with 95% confidence interval and 80% power.DiscussionAyurveda treatsSantarpanottha(originated from over nutrition) symptoms andApatarpanottha(symptoms originated from undernutrition) symptoms differently; hence, inspite of the same disease or symptom management, changes depend upon the type of the origin. This pragmatic clinical study is developed on the fundamental grounds of Ayurveda.Ethics and disseminationEthics approval was obtained through the Institutional Ethics Committees of Government Ayurved College and Hospital on 23 July 2021.Trial registrationThe trial is prospectively registered with the Clinical Trial Registry of India on 17 August 2021 [CTRI/2021/08/035732] after the Institutional Ethics Committee approval [GACN/PGS/Synopsis/800/2021 Date 23/7/2021].Supplementary InformationThe online version contains supplementary material available at 10.1186/s40814-023-01322-1.