Dhoni surpassed Gilchrist during the fourth ODI against West Indies when he scored 78 runs.
He is currently standing in the second position with 9496 runs.
Gilchrist had scored 9410 ODI runs in his career.
Congratulating him, Gilchrist posted on Instagram: "Congrats on passing me young fella. Was always a matter of time. #msd#2ndhighest #keepers."
With 14234 ODI runs, Sri Lanka's Kumar Sangakkara is currently at the top of the chart.
MS Dhoni is considered as one of the greatest finishers in the game.
He had captained India in winning T20 World Cup in 2007 and the World Cup in 2011.
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