Mokhtar Lamani, who heads Brahimi's Damascus office, "has submitted a request to the United Nations to be relieved of his duties, but he has not officially resigned," UN spokesman Khaled al-Masri told AFP.
The spokesman did not provide an explanation for Lamani's decision.
He was appointed to represent Brahimi in Damascus in September 2012.
Lamani had expressed his disappointment with the failed Geneva II talks that brought together regime and opposition representatives in two separate rounds in January and February, but reaped no concrete result.
Lamani has held frequent meetings with both rebel and regime representatives, shuttling across battle lines in Syria, and has a very strong grasp of the situation on the ground.
Brahimi took over from his predecessor, Kofi Annan, as UN-Arab League peace envoy to Syria in September 2012.
Lamani is of Moroccan origin and speaks Arabic fluently. He is said to be a good listener who expresses his views openly to both sides in the war.
Lamani was also Arab League representative to Iraq from 2006 to 2007, but resigned after announcing he could not fulfil the demands of his post.
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