Abstract A nighttime electrified medium‐scale traveling ionospheric disturbance (EMSTID) was observed over Japan on 17 March 2003, after two moderate geomagnetic storms. Unlike typical northwest‐southeast alignment in quiet conditions, the EMSTID exhibited an unusual northeast‐southwest orientation. Challenging Minisatellite Payload neutral wind and ROCSAT‐1 ion drift measurements showed significant thermospheric wind and electric field variations from quiet‐times. The study reveals a unique disturbance dynamo‐driven electrodynamical mechanism that triggers Perkins instability, generating unusually aligned nighttime EMSTID. Notably, low electron density and weak inhomogeneity in sporadic‐E layers in both locally (Wakkanai, Japan) and over conjugate regions (Townsville, Australia) reveal that Perkins instability can be enhanced sufficiently to generate EMSTIDs, even with weak E‐F regions coupling within or across hemispheres. Additionally, penetration electric fields during a substorm’s expansion and recovery phases instantaneously modulated EMSTID amplitudes. Such nighttime EMSTID, comprising unique features and near‐instantaneous amplitude modulation caused by substorm‐induced electric fields, represents the novel observation of this study.

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