Jet schemes and arc spaces received quite a lot of attention by researchers after their introduction, due to J. Nash, and established their importance as an object of study in M. Kontsevichs motivic integration theory. Several results point out that jet schemes carry a rich amount of geometrical information about the original object they stem from, whereas, from an algebraic point of view, little is know about them. In this paper we study some algebraic properties of jet schemes ideals of pfaffian varieties and we determine under which conditions the corresponding jet scheme varieties are irreducible.