She has conducted research into the use of soil microbes for use in medicine, including applications in the development of new antibiotics.
In recognition for her work, she was one of five young scientists from the developing countries who received the Elsevier Foundation Award in 2016.
For her PhD from Sun Moon University, Korea, in 2011, she pursued her interest in metabolic and genetic engineering, focusing on streptomycetes.
She has also sought to improve the teaching of science in Nepal by encouraging her students to work in research laboratories where they can put theory into practice.
[4] As of April 2018, Maharjan is applying an organ-on-a-chip approach to the establishment of differences between the sexes to diseases in her role as a post-doctoral research fellow at the Brigham and Women's Hospital in Boston.