In the past 5years, aggregation-induced emission luminogens (AIEgens) with emission in the second near-infrared (NIR-II) optical window have aroused great interest in bioimaging and disease phototheranostics, benefiting from the merits of deep penetration depth, reduced light scatting, high spatial resolution, and minimal photodamage. To construct NIR-II AIEgens, thiophene derivatives are frequently adopted as π-bridge by virtue of their electron-rich feature and good modifiability. Herein, we summarize the recent progress of NIR-II AIEgens by employing thiophene derivatives as π-bridge mainly compassing unsubstituted thiophene, alkyl thiophene, 3,4-ethylenedioxythiophene, and benzo[c]thiophene, with a discussion on their structure-property relationships and biomedical applications. Finally, a brief conclusion and perspective on this fascinating area are offered.