Ramanathan is an ISI highly cited researcher. He is a fellow of the American Association for the Advancement of Science, American Meteorological Society and American Geophysical Union. He became a member of the American Academy of Arts and Sciences in 1995. In 1995, the Royal Netherlands Academy of Arts and Sciences awarded him the Buys Ballot Medal. In 2002, he was awarded the Carl-Gustaf Rossby Research Medal, "... for fundamental insights into the radiative roles of clouds, aerosols and key gases in the Earth's climate system." He was elected a member of the US National Academy of Sciences in 2002 "... for fundamental contributions to our modern understanding of global climate change and human impacts on climate and environment", an Academician of the Pontifical Academy of Sciences in 2004, a member the American Philosophical Society in 2006, and a member of the Royal Swedish Academy of Sciences in 2008.
Also, Veerabhadran Ramanathan has been bestowed with the BBVA Foundation Frontiers of Knowledge Award 2015 in the Climate Change category for discovering that human-produced gases and pollutants other than  have a huge power to alter the Earth's climate, and that by acting on them it is possible to make a short-term dent on the rate of global warming. He received the prestigious Tang Prize for Sustainable Development in 2018. He was awarded the 90th annual Mendel Medal by Villanova University in 2018 for his work on climate change. Ramanathan is the recipient of the Lifetime Achievement Award (Champions of the Earth) in 2013.