X-ray timing properties of the magnetar SGR 1900+14 were studied, using the data taken with Suzaku in 2009 and NuSTAR in 2016, for a time lapse of 114 ks and 242 ks, respectively. On both occasions, the object exhibited the characteristic two-component spectrum. The soft component, dominant in energies below ∼ 5 keV, showed a regular pulsation, with a period of P = 5.21006 s as determined with the Suzaku XIS, and P = 5.22669 with NuSTAR. However, in 6 keV where the hard component dominates, the pulsation became detectable with the Suzaku HXD and NuSTAR, only after the data were corrected for periodic pulse-phase modulation, with a period of T = 40 − 44 ks and an amplitude of ≈ 1 s. Further correcting the two data sets for complex energy dependences in the phase-modulation parameters, the hard X-ray pulsation became fully detectable, in 12-50 keV with the HXD, and 6-60 keV with NuSTAR, using a common value of T = 40.5 ± 0.8 ks. Thus, SGR 1900+14 becomes a third example, after 4U 0142+61 and 1E 1547−5408, to show the hard X-ray pulse-phase modulation, and a second case of energy dependences in the modulation parameters. The neutron star in this system is inferred to perform free precession, as it is axial deformed by ≈ P/T = 1.3 × 10 −4 presumably due to ∼ 10 16 G toroidal magnetic fields. As a counter example, the Suzaku data of the binary pulsar 4U 1626−67 were analyzed, but no similar effect was found. These results altogether argue against the accretion scenario for magnetars.