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Abstract Ionospheric scintillations due to plasma irregularities can severely affect the modern dynamic and technological systems whose operations rely on satellite-based navigation systems. We investigate the occurrence of ionospheric scintillation in the equatorial and low latitude region over Malaysia after the 2011 Valentine’s Day solar flare. A network of three Global Ionospheric Scintillation and Total Electron Content Monitor (GISTM) GSV4004B receivers with increasing latitudes from the magnetic equator were used to monitor ionospheric TEC, rate of change of TEC index (ROTI), and amplitude (S4) as well as phase (σ φ) scintillation indices. The results show a simultaneous sudden rise in S4 and σ φ along with a significant depletion of TEC at all three locations. However, the largest enhancement of scintillation indices accompanying a substantial TEC depletion is observed at the farthest low latitude station (UNIMAS) from the equator with values around 0.5, 0.3 rad, and 1 TECU, respectively. The corresponding values at the near-equatorial station (Langkawi; 0.4, 0.2 rad, and 3 TECU) and intermediate station (UKM; 0.45, 0.3 rad, and 5 TECU) are examined along with ROTI variations, confirming the simultaneous occurrence of kilometer-scale and sub kilometer scale irregularities during 17 and 18 February 2011. The radiation effects of the solar flare on the ionosphere were prominently recognized at the local nighttime hours (around 14:00 to 17:00 UT) coinciding with the equatorial prereversal enhancement (PRE) time to seed the equatorial plasma bubbles (EPBs) enhancement that resulted in ionospheric irregularities over the low latitudes. The significant TEC depletion seen in the signals from selected GPS satellites (PRNs 11, 19, 23, and 32) suggests plausible degradation in the performance of GPS-based services over the Malaysian region. The study provides an effective understanding of the post-flare ionospheric irregularities during an episode of minor geomagnetic storm period and aligns with the efforts for mitigating the scintillation effects in space-based radio services over low latitudes.