The leadership of the union is based a structure contained in her constitution. The top policy organ of union is the National Executive Council (NEC). The NEC is composed of 28 members, of whom eight are the top national officials and the rest are drawn from province as follows:- Nairobi and North Eastern (one each), Coast (two), Eastern, Central, Western and Nyanza (three each), Rift Valley (Four) and two women representatives. Three Trustees also sit in the NEC as ex-officio members without voting powers.

The eight top officials work full time at the KNUE Head Office and constitute the National Steering Committee. The Steering Committee is responsible to the NEC for management of union affairs besides the coordination and supervision of branch activities.

The NEC is responsible for all policy issues – formulation, implementation and monitoring and reports to the Annual Delegates Conference (ADC).

The leadership at the branch level is composed a Branch Steering Committee of five members, one or two women representatives and members representing designated zones. The groups constitute the Branch Executive Committees (BEC).

Between the BEC and NEC are the Provincial Councils (PCs). A provincial council is composed of the top three leaders (Chairman, Executive Secretary and Treasurer) from all the branches in the province and all the NEC members from the province even if they are not amongst the top three branch leaders.

The ADC which is the supreme organ of the union is convened once a year to deal with any issue placed before it by the NEC. The delegates and constituted by inviting every branch to nominate one delegate for every 100 members enrolled in the branch.