Functional genomics represents the methods used in unravelling the genetic basis of complex factors such as fruit development, ripening, quality, disease resistance, and stress tolerance. Traditional genetic practices, primarily via stable transformation, are often limited by the long generation times and recalcitrant genetics of many fruit crops. A faster, more efficient reverse genetics tool known as virus-induced gene silencing was developed to target genes by transient suppression through the plant’s innate RNA silencing pathways without the need for stable transgenic lines. With a focus on tobacco rattle virus (TRV), this chapter presents a detailed overview of VIGS technology and its utilization mainly in apple, strawberry, grapevine, peach, cherry, and citrus, covering the development and optimization of viral vectors. There are also some remarkable insights into important biological pathways like fruit ripening regulation, pigment biosynthesis, hormone signalling, and plant defence processes that are gained using VIGS-assisted gene silencing. In addition to recent developments improving VIGS specificity and robustness, this chapter also discusses practical issues like host specificity, off-target effects, and inconsistent silencing efficiency. Additionally, this chapter examines the new trend of combining VIGS with genome editing and innovative delivery methods, highlighting the potential of VIGS to speed up gene function analysis and molecular breeding to improve fruit crop quality and productivity.