Expressions of various neurotrophic factors or their receptors fluctuate after stroke, which in part prompted investigations into the efficacy of neurotrophic factors as treatment modality for stroke. The methods to deliver neurotrophic factors into the brain can be categorized into: 1) the surgical route of administration, such as intracerebral, intraventricular, intra-arterial, or intravenous systemic administration and 2) the manipulation of the therapeutic molecules via ex vivo or in vivo techniques. With ex vivo method, genetically engineered cells, including the use of autologous cells, have been explored. In this review, the potent therapeutic applications of neurotrophic factors in stroke are described, with emphasis on ex vivo methods, especially transplantation of encapsulated stem cells modified with adenovirus. Neurotrophic factor delivery, combined with ex vivo method, poses as novel treatment for stroke, although additional safety and efficacy studies remain to be examined.