From 1997 to 2001, Siddiqui served in various capacities in the Clinton administration at US Department of Agriculture as Under Secretary for Marketing and Regulatory Programmes, Senior Trade Advisor to Secretary Dan Glickman and Deputy Under Secretary for Marketing and Regulatory Programmes.

As a result, he worked closely with the USTR and represented USDA in bilateral, regional and multilateral agricultural trade negotiations.

Since 2004, Siddiqui has also served on the US Department of Commerce's Industry Trade Advisory Committee on Chemicals, Pharmaceuticals, and Health/Science Products & Services, which advises the US Secretary of Commerce and USTR on international trade issues related to these sectors.

Between 2001 and 2003, Siddiqui was senior associate at the Centre for Strategic and International Studies (CSIS), where he focused on agricultural biotechnology and food security issues.

Before joining USDA, Siddiqui spent 28 years with the California Department of Food and Agriculture.