James Dobbins, a veteran diplomat with deep ties to Afghanistan, is retiring after just over a year in office and will be replaced by his deputy Dan Feldman, Kerry said in a statement.
The shuffle comes as the two candidates to be Afghanistan's next president -- succeeding Hamid Karzai who has held the reins for 13 years -- wrangle over alleged fraud in the elections.
The political crisis threatens the country's first democratic transfer of power, and tarnishes US hopes of a smooth handover as it prepares to withdraw all US forces by late 2016.
The veteran diplomat, who came out of retirement to take up the post in May 2013, has steered negotiations to draw up a security pact to safeguard US troops staying in Afghanistan beyond this year.
After Karzai refused at the 11th hour to sign the deal, both presidential candidates said they would Honor the negotiations and accept the bilateral security agreement (BSA).
US President Barack Obama announced in May that US forces would complete their withdrawal from Afghanistan in 2016, ending more than a decade of war which followed the 2001 US invasion to oust the hardline Islamic Taliban government.
Dobbins "has played an out sized role on the ground negotiating the BSA, making preparations for historic elections, growing our counterterrorism cooperation with Pakistan, and planning for a transition for the Afghan people after more than a decade of progress," Kerry said.
He will be "forever known as the guy who raised the first flag over our embassy in Kabul after the fall of the Taliban," Kerry added.
Feldman will now take over the post once held by the charismatic diplomat Richard Holbrooke, who had brought him on board as deputy special representative for Afghanistan and Pakistan in 2009.
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