As part of her training, from 1987 to 1989 Swaminathan completed a post-doctoral medical fellowship in neonatology and pediatric pulmonology at the Children's Hospital Los Angeles at the Keck School of Medicine of USC.

[3][4] In March 2019, Swaminathan became chief scientist of the World Health Organization, where she notably participated in regular twice weekly press briefings on the COVID-19 pandemic.

[13] In the preparations for the Global Health Summit hosted by the European Commission and the G20 in May 2021, Swaminathan was a member of the event's High Level Scientific Panel.

[9][15] While at the National Institute for Research in Tuberculosis in Chennai, Swaminathan started a multi-disciplinary group of clinical, laboratory and behavioural scientists studying various aspects of TB and TB/HIV.

[16] She was part of the TB Zero City Project which aimed to create "Islands of elimination" working with local governments, institutions and grassroots associations.

[17][18] In 2021, Swaminathan was also appointed to the Pandemic Preparedness Partnership (PPP), an expert group chaired by Patrick Vallance to advise the G7 presidency held by the government of Prime Minister Boris Johnson.