A method for performing a shuttle shift with a transmission of a work vehicle is disclosed, wherein the transmission includes an input shaft, a counter shaft and a plurality of driven shafts extending generally parallel to the input and counter shafts. The method may include disengaging a clutch associated with a first directional gear of a directional shaft of the plurality of driven shafts. The first directional gear may be configured to rotate the directional shaft in a first direction. Additionally, the method may include engaging clutches associated with at least two gears of at least one secondary driven shaft of the plurality of driven shafts to reduce a rotational speed of the directional shaft and, after the rotational speed of the directional shaft is reduced, engaging a clutch associated with a second directional gear of the directional shaft such that the directional shaft rotates in a second direction.