Small fish species that have no commercial value are often overlooked in conservation management, despite serious concerns about their long-term future. The Nannoperca australis (southern pygmy perch) of temperate south eastern Australia is representative of many small freshwater fishes. We develop a structured population model for this species to assess risk of localised extinction and assist in the decision making for their conservation management in NSW, Australia. The objectives of this study were threefold: to develop a stochastic population model for Nannoperca australis; to determine what constitutes a viable population for the species; and to use the model to provide guidance for the establishment of new populations, assess the impacts on donor populations, and consider other conservation management actions. The model was sensitive to the estimation of early life history survival for which there are no estimates from field data. Given uncertainty in some vital rates, the modelling indicates that a population in stable habitat that would be expected to support 2000 female adults would be likely to be viable and able to withstand some disturbance and possibly be used as a source population for reintroductions, however it was found that with multiple disturbances and being used as a source population generates an 7.9% risk or extinction. A larger stable habitat expected to support 8000 females with multiple disturbances and being used as a source population generates a 2.4% risk of extinction. A stable habitat expect to support 500 female adults may not be viable as multiple disturbances together with being used as a source population generates a substantial risk of extinction of 24% and a very high probability of being small, Pr(minimum population size ≤ 25) = 71%. If suitable habitat can be found or established, releasing 1000 female adults over 5 years would likely result in the establishment of a viable population. The model allows for a variety of reintroduction strategies to be tested as well as other management options. This type of approach can be used to improve the conservation management of many similar species worldwide.