Banerjee, who is on a five-day visit to the UK, was meeting Prince Andrew, Queen Elizabeth II's second son and UK's special representative for international trade and investment, at Buckingham Palace when the news of Kalam's death broke.
"Very, very sad news. I had a special bond with Kalamji. He was one of India's favourite sons and one of my favourite people. A very sad day," she said on Twitter.
From the palace, Banerjee went on to meet Priti Patel, the UK's Minister of State for Employment and British Prime Minister David Cameron's Indian Diaspora Champion, at the Foreign and Commonwealth Office (FCO) where 21 MoUs were signed across the fields of industry, health, education and urban development.
Kalam served as the President of India from 2002 to 2007.