His mother obtained a PhD in Psychology from McGill University in 1959. completing it in only 18 months, and was mentored by Donald O. Hebb. Lalita Ramakrishnan, his younger sister, is professor of immunology and infectious diseases at the Department of Medicine, University of Cambridge, and is a member of the National Academy of Sciences.

Ramakrishnan moved to Vadodara (previously also known as Baroda) in Gujarat at the age of three, where he had his schooling at Convent of Jesus and Mary, except for spending 1960–61 in Adelaide, Australia. Following his pre-science at the Maharaja Sayajirao University of Baroda, he did his undergraduate studies in the same university on a National Science Talent Scholarship, graduating with a Bachelor of Science degree in Physics in 1971. At the time, the physics course at Baroda was new, and based in part on The Berkeley Physics Course and The Feynman Lectures on Physics.

Ramakrishnan married Vera Rosenberry, an author and illustrator of children’s books, in 1975. His stepdaughter, Tanya Kapka, is a doctor in Oregon, and his son, Raman Ramakrishnan, is a cellist based in New York.

Immediately after graduation he moved to the U.S., where he obtained his Doctor of Philosophy degree in Physics from Ohio University in 1976 for research into the ferroelectric phase transition of potassium dihydrogen phosphate (KDP) supervised by Tomoyasu Tanaka. Then he spent two years studying biology as a graduate student at the University of California, San Diego while making a transition from theoretical physics to biology.

He continued to work on ribosomes from 1983-95 as a staff scientist at Brookhaven National Laboratory. In 1995 he moved to the University of Utah as a Professor of Biochemistry, and in 1999, he moved to his current position at the Medical Research Council Laboratory of Molecular Biology in Cambridge, England, where he had also been a sabbatical visitor during 1991-92 on a Guggenheim Fellowship.

In 1999, Ramakrishnan’s laboratory published a 5.5 angstrom resolution structure of the 30S subunit. The following year, his laboratory determined the complete molecular structure of the 30S subunit of the ribosome and its complexes with several antibiotics. This was followed by studies that provided structural insights into the mechanism that ensures the fidelity of protein biosynthesis. In 2007, his laboratory determined the atomic structure of the whole ribosome in complex with its tRNA and mRNA ligands. Since 2013, he has primarily used cryo-EM to determine new ribosome structures. Ramakrishnan is also known for his past work on histone and chromatin structure.

Ramakrishnan was elected a Member of the European Molecular Biology Organization (EMBO) in 2002, a Fellow of the Royal Society (FRS) in 2003, and a Member of the U.S. National Academy of Sciences in 2004. In 2007, Ramakrishnan was awarded the Louis-Jeantet Prize for Medicine and the Datta Lectureship and Medal of the Federation of European Biochemical Societies (FEBS). In 2008, he won the Heatley Medal of the British Biochemical Society. Since 2008, he is a Fellow of Trinity College, Cambridge and a foreign Fellow of the Indian National Science Academy. He was elected an Honorary Fellow of the Academy of Medical Sciences in 2010, and has received honorary degrees from the Maharaja Sayajirao University of Baroda, University of Utah and University of Cambridge. He is also an Honorary Fellow of Somerville College, Oxford. In 2020 he was elected to the American Philosophical Society. Also in 2020, he became a board member of The British Library.

In 2009, Ramakrishnan was awarded the Nobel Prize in Chemistry along with Thomas A. Steitz and Ada Yonath. He received India’s second highest civilian honor, the Padma Vibhushan, in 2010. Ramakrishnan was knighted in the 2012 New Year Honours for services to Molecular Biology, but does not generally use the title “Sir”. In the same year, he was awarded the Sir Hans Krebs Medal by the FEBS. In 2014, he was awarded the XLVI Jiménez-Díaz Prize by the Fundación Conchita Rábago (Spain). In 2017, Ramakrishnan received the Golden Plate Award of the American Academy of Achievement. Ramakrishnan was included as one of 25 Greatest Global Living Indians by NDTV Channel, India on 14 December 2013. His certificate of election to the Royal Society reads:

In an interview in July 2018, he said that Britain’s decision to leave the European Union (Brexit) was hurting Britain’s reputation as a good place to work in science, commenting “It’s very hard for the science community to see any advantages in Brexit. They are pretty blunt about that.” He saw advantages to both the UK and the EU for Britain to continue to be engaged in Galileo and Euratom, which, unlike the European Medicines Agency, are not EU agencies.

As of 2019 his most cited papers (according to Google Scholar) have been published in Nature, Science, and Cell.