The nature of intraseasonal (within a season) variability of the nighttime ionospheric irregularities has been studied utilizing the observation of the recently installed VHF scintillation receiver from Pingtung, Taiwan. Investigation is based on observations made in 2015 (high-moderate solar epoch) and 2017 (low solar epoch). Detailed investigation has revealed coexistence of planetary-scale variability (3–7 days), 10- to 16-day variability, and > 25-day variability in 2015. Interestingly, the Lomb-Scargle frequency domain analysis indicated the variability of larger timescales to display somewhat greater amplitudes. The virtual height of the F layer, h'F, over Sanya, also indicated intraseasonal periodicities similar to S4 periodicities observed at Pingtung. Observations have also revealed that, equatorial plasma bubbles (EPBs) over Pingtung tended to occur on contiguous nights as compared to isolated occurrence, and > 60% of the EPB nights were part of two or more (up to 6) nights of contiguous occurrence. Spectral analysis revealed a quasi-27-day variability in the ap and AE geomagnetic indices presumably associated with the solar rotation period. The time period of geomagnetic variability corresponded with the period of dominant S4 variability, indicating that the effect of geomagnetic activity on the low-latitude ionosphere can be periodic in nature. In 2017 (low solar flux), even with a very low occurrence of ionospheric irregularities, planetary-scale variability was observed. The dominant period of S4 variability in the autumnal equinox was highly correlated with the periodic geomagnetic activity. Results indicate that a deeper understanding of the periodic intraseasonal variability can be imperative for extended range forecast/prediction of ionospheric irregularities.