We develop the framework of boundary derivative expansion (BDE) formalism of fluid/gravity correspondence in a compactified D4-brane system, which is a nonconformal background used in top-down holographic QCD models. Such models contain the D4-D6 model and the Sakai-Sugimoto (SS) model, with the background of the compactified black D4 branes under the near-horizon limit. By using the dimensional reduction technique, we derive a 5D Einstein gravity minimally coupled with three scalar fields from the 10D D4-brane background. Following the BDE formalism of fluid/gravity correspondence in the conformal background, we directly derive all the first order transport coefficients for nonconformal gluonic matter. The results of the ratio of the bulk to shear viscosity and the sound speed agree with those obtained from the Green-Kubo method. This agreement guarantees the validity of the BDE formalism of fluid/gravity duality in the nonconformal D-brane background, which can be used to calculate the second order transport coefficients in nonconformal background.