Amphioxi represent the evolutionary link between vertebrates and invertebrates. For this reason, research dealing with these animals has been focused mainly on embryological and anatomical studies. Out of 30 described species, only one, Branchiostoma elongatum, is known to inhabit shallow sandy bottoms along the Humboldt Current System (HCS) of Chile and Peru. The population dynamics of B. elongatum from northern Chile was studied between February 2008 and January 2009, and the results were compared with other species within the genus Branchiostoma inhabiting distinct ecosystems. Mean abundance of B. elongatum was low (158.6 ind m−2) in comparison with the abundance of other species within Branchiostoma. Although the gametogenic activity was continuous, a clear spawning event was observed between August and October, which seemingly produced a recruitment pulse during the summer and consequently a simultaneous increase in population density and decrease of mean length during that period. Growth of B. elongatum was best fitted to the seasonalized von Bertalanffy growth function (K = 0.45 year−1 and L∞ = 64.6 mm), with faster growth during summer–autumn. Growth performance (Ф′ = 3.273) was high in comparison with other species within the genus. Mortality of B. elongatum (Z = 1.075 year−1) was well fitted to the single exponential model (r2 = 0.92). The annual total production of B. elongatum reached 0.68 g ash-free dry mass (AFDM) m−2 and the annual mean biomass was 0.56 g AFDM m−2, which determined a production to biomass ratio of 1.22. The huge productivity of the HCS was not reflected in a high abundance and biomass of B. elongatum. However, this species displayed a high growth efficiency and P/B ratio that are comparable to those of other Branchiostoma inhabiting highly productive ecosystems.