We study Pandharipande-Thomas's stable pair theory on K3 fibrations over curves with possibly nodal fibers. We describe stable pair invariants of the fiberwise irreducible curve classes in terms of Kawai-Yoshioka's formula for the Euler characteristics of moduli spaces of stable pairs on K3 surfaces and Noether-Lefschetz numbers of the fibration. Moreover, we investigate the relation of these invariants with the perverse (non-commutative) stable pair invariants of the K3 fibration. In the case

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... hat the K3 fibration is a projective Calabi-Yau threefold, by means of wall-crossing techniques, we write the stable pair invariants in terms of the generalized Donaldson-Thomas invariants of 2-dimensional Gieseker semistable sheaves supported on the fibers.