In 2002, after completing her specialist training, Zaidi returned to
Pakistan. She was one of the youngest faculty members to be promoted to full professor when she became chair of the Department of Paediatrics and Child Health at
Aga Khan University. In 2011 she was awarded an endowed position; the Ruby and Karim Bahudar Ali Jessani Professor and Chair. At
Aga Khan University Zaidi established a state-of-the-art laboratory that investigates paediatric infectious diseases. She was the first recipient of the Caplow's Children's Prize for her work supporting poverty-stricken communities in
Karachi in 2013. She used the prize to reduce neonatal deaths in
Rehri Goth. Her efforts focussed on eliminating malnutrition, improving access to healthcare and vaccinations and training for community health professionals. She developed programs that supported mother and child health before, during and after children were born. Zaidi estimated that the program would reduce child mortality by 65%, saving the lives of 200 children over two years. In this capacity Zaidi supports the development of new vaccinations to protect communities around the world. In June 2020 the Gates Foundation announced a new division dedicated to gender equality, with Zaidi being its first president. As of March 2021, Zaidi still also directs Vaccine Development, Surveillance, Diarrhea and Enteric Diseases at the Foundation. Zaidi uses
social media to share her work in
public health using the Twitter handle @AnitaEDD. She has written for
The Conversation, the
Skoll Foundation,
Project Syndicate and
HuffPost. ==Other activities==