The 47-year-old Serbian confirmed he was terminating his contract with the Cranes in a row over unpaid salary allowances totalling 216 million shillings ($64,000).
“I have been patient and working under very difficult conditions. Today I have resigned because I and FUFA (Federation of Uganda Football Association) have stretched limits,” Sredojevic told AFP on Saturday.
FUFA president Moses Magogo confirmed the departure of the Serbian coach after four years in charge of the national team.
Sredojevic joined the Cranes in May 2013 after being sacked as the head coach of Rwanda, and successfully qualified Uganda for their first Cup of Nations since 1978.
Uganda were knocked out in the first round of the tournament held in Gabon after two losses and a draw in Group D. They are still in contention to qualify for next year’s World Cup in Russia, with a key game in Egypt to come next month.