Detrimental effects of the equatorial ionospheric irregularities on satellite-based communication and navigation systems have been studied over the past few decades as space weather events have the potential to seriously disturb the technological infrastructure of modern society. The present paper tries to understand operational compliance of Global Positioning System (GPS) receivers to International Civil Aviation Organization (ICAO) standards under scintillation conditions by recording the received phase of the L1(1575.42 MHz) signal from two stations, namely Calcutta situated near the northern crest of the Equatorial Ionization Anomaly and Siliguri, situated beyond the northern crest, at a subionospheric latitude separation of 4° along the same meridian. A causative approach is adopted whereby GPS phase scintillations have been monitored and receiver performance prior to loss of lock and cycle slips have been analyzed during August–October 2011 at Calcutta and September 2011 at Siliguri. The received phase at GPS-L1 frequency has often been found to fluctuate at kilohertz, often megahertz rates, thereby causing carrier-tracking loop malfunctions. It should be borne in mind that normal GPS receivers' carrier-tracking loops have a typical dynamic range of 14–18 Hz. Cycle slips have been observed with durations far exceeding ICAO specified levels for high dynamic platforms like aircrafts. Differences in cycle slips between Calcutta and Siliguri indicate possible evolution of irregularity structures even across small subionospheric swath. Significant improvement in present understanding of GPS phase scintillations should be developed and implemented in receiver designs prior to application of Satellite Based Augmentation System services for civil aviation, particularly in the geophysically sensitive equatorial region.