J-aggregation has been proved to be an efficient strategy for the development of fluorescent imaging agents in the second near-infrared (NIR-II, 1000–1700 nm) window. However, the design of NIR-II fluorescent J-aggregates is challenging due to the lack of suitable J-aggregation dyes. Herein, we report meso-[2.2]paracyclophanyl-3,5-bis-N,N-dimethylaminostyrl BODIPY (PCP-BDP2) as the first example of BODIPY dye with J-aggregation induced NIR-II fluorescence. PCP-BDP2 shows emission maximum at 795 nm in diluted solution and NIR-II emission at 1010 nm in the J-aggregation state. Mechanism studies reveal that the steric and conjugation effect of the PCP group on the BODIPY core plays key roles in the J-aggregation behavior and NIR-II fluorescence tuning. Notably, NIR-II emissive J-aggregates of PCP-BDP2 can be efficiently stabilized in the assembled nanoparticle. Taking advantage of high quantum yield and good photo-/chemo-stability, J-aggregates of PCP-BDP2 show high-resolution and long-term in vivo NIR-II imaging ability. Furthermore, J-aggregates of PCP-BDP2 can be utilized for lymph node imaging and fluorescence-guided surgery in the nude mouse, which demonstrates their potential clinical application. This study not only demonstrates BODIPY dye as a new J-aggregation platform for developing NIR-II imaging agents but also encourages further exploration on J-aggregation induced NIR-II emission of the other conventional organic dyes.