The Scot had a contract with the side up to September 2014, but the Federation of Uganda Football Associations has decided to release him early following the 2-0 World Cup qualifier loss to Liberia last month.
"FUFA hereby informs the public that a notice of termination of contract has this morning Monday 8th April 2013 has been given to the Cranes head coach Mr Robert 'Bobby' Williamson," a statement from the organisation read.
The 51-year-old took over as Uganda manager in July 2008 and led them to three regional CECAFA titles in 2010, 2012 and 2013.
He also took the side to the brink of qualification for the 2013 African Nations Cup before losing out 9-8 in a dramatic penalty shootout in their final qualifier against then African champions Zambia.
Uganda are bottom of their World Cup qualification pool but only three points behind leaders Senegal and with home matches against Liberia and Angola to come in June.
- Sports & Recreation