Andrew Mackenzie, the head of its base metals business, will replace Mr Kloppers in May.
The announcement came as Anglo-Australian mining giant BHP reported a 43pc drop in half-year profit, its worst half-year slide in more than a decade, as expected, pummelled by weaker metals prices.
It also booked $3bn in writedowns on its Worsley alumina and Nickel West assets, matching analysts forecasts, as aluminium prices have slumped due to a sharp increase in Chinese supply that global producers failed to anticipate.
Mr Mackenzie, 56, who joined BHP from rival Rio Tinto (Xetra: 855018 - news) in 2008, will be taking over as the company battles to protect margins by reining in costs in a weaker commodity pricing environment.
"The board has decided that Andrew is the right person to lead BHP Billiton in a changing global environment," the company said in a statement.
BHP last year shelved $40bn in projects and shut some loss-making coal mines, as the industry battled with soaring costs, a strong Aussie dollar and sliding commodity prices.
In further moves to protect its margins, it said on Wednesday it had cut $944m in costs over the past half year.
Profit before one-off items slid to $5.68bn for July-December 2012 from $10bn a year earlier. The result was in line with analysts' average forecast for a profit of $5.69bn.
Net profit fell to $4.2bn, with the aluminium and nickel writedowns offset by gains from the sales of its Richards Bay minerals stake, its Browse gas stake, its diamonds business and Yeelirie uranium deposit.
BHP raised its interim dividend by 3.6pc to 57 cents, also in line with analysts' forecasts, Reuters reported.
Rival Rio Tinto last week reported its first ever full-year loss after taking $14.4bn in writedowns on its aluminium business and Mozambican coal assets, but appeased investors with a surprise 15pc rise in its annual dividend.