Mukherjee said in his message that he was deeply concerned to learn the recent indisposition of the UAE Head of the State, a statement from Rashtrapati Bhavan said.
"I do hope that you are feeling better by now and progressing rapidly on the path of recovery," he said.
Lauding UAE President's valuable personal contribution to India-UAE relationship, Mukherjee said it has enhanced mutual understanding between the two countries and brought the two peoples closer to each other.
Sheikh Khalifa became President of the United Arab Emirates and ruler of the oil-rich emirate of Abu Dhabi in November 2004, when he succeeded his late father Sheikh Zayed bin Sultan, who founded the Emirati federation in 1971.
Sheikh Khalifa, 66, who is also ruler of oil-rich Abu Dhabi, has not made a public appearance since the UAE announced that he underwent an operation following a stroke on January 24.