In hospitals, IV bags can be prepared in advance for logistical and microbial safety reasons in a compounding unit and then transported to wards. Transport of protein drugs using a pneumatic tube system has been reported to result in high particle levels. In this study, pneumatic tube transport of trastuzumab in saline polyolefin bags was compared to delivery by hospital porters using an electric platform truck in an underground tunnel system. The transport was tracked using designed smart labels. Two strategies to prevent particle formation, removing headspace and adding the surfactant polysorbate 20 were evaluated. The transport by pneumatic tube had a higher level of shock and vibration than truck delivery. The total particle count measured using flow microscopy also increased more for pneumatic transport than for transport by vehicle. Removing the headspace decreased particle formation for both transports. Surfactant decreases particles over 10 µm for trastuzumab in saline IV bags but increases the total particle levels. Pneumatic tube transport of saline in polyolefin bags resulted in high particle levels and surfactant increased the total particle count. Removing headspace is a measure that can be incorporated into compounding practices to cover for inadequate surfactant levels in IV bags.