Sodium cyanoborohydride (CBH) is commonly used as a mild reducing agent in the reductive amination of aldehydes and free amines. Within the pharmaceutical industry, this reaction is employed in the bioconjugation of proteins and peptides. Free cyanide species such as HCN and NaCN are known residual impurities in CBH that can contribute to the formation of undesired side products including cyanoamines and cyanohydrins. In commercial processes, the potential for bound cyanated species requires an analytical control strategy to monitor and mitigate any risk to human health. Given these concerns, minimization of cyanated side products is of utmost priority and can be achieved through a robust control strategy of quantitative screening of starting materials for free cyanide. Alternative risk mitigation strategies such as purification of bound cyanide containing species to pure species are less effective due to minor chemical differences between the expected product and bound cyanide species. Herein, we present a simple chromatographic assay for the quantitation of free cyanide in the raw material sodium cyanoborohydride. Method development, robustness evaluation, and scientific soundness assessment are reported with excellent linearity, accuracy, precision, and specificity. Additionally, this method was applied for the evaluation of raw material supplied from 10 commercial sources, none of which report a specification for free cyanide within their certificate of analysis. The measured free cyanide from these vendors ranged from 8 to 80 mM concentration, thereby confirming the value of screening these raw materials. Finally, we demonstrate the impact of free cyanide on a model bioconjugation reaction between ornithine and glyceraldehyde.