Recent efforts on manipulating metal nanoparticles (NPs) using an electron beam have offered new insights into nanoparticle behavior, structural transition, and the emergence of new properties. Despite an increasing understanding of the dynamics of electron beam‐induced coalescence of NPs, several phenomena are yet to be investigated. Here, we show that repulsion between two NPs is as favorable as coalescence under electron beam irradiation at room temperature. Using small‐sized (D ≈ 5.9 nm) and large‐sized (D ≈ 11.0 nm) gold (Au) NPs, and different electron dose rates, a unique sequential attraction‐repulsion between NPs is disclosed. The real‐time in situ transmission electron microscopy imaging suggest that at a low dose rate, two small‐sized AuNPs with 1.0 nm particle–particle distance undergo repulsion to 18 nm with a diffusion rate of 0.4 nm min−1. For large‐sized AuNPs, the repulsion rate is 0.08 nm min−1 at a low dose rate and is comparable to that of small‐sized AuNPs at a high dose rate. Surprisingly, large‐sized AuNPs at a high electron dose rate displayed attraction in the first 15 min, followed by rapid repulsion. This unique sequential attraction‐repulsion behavior of NPs offers possibilities to manipulate interparticle distance and properties without inducing dimensional changes for advanced photonic and plasmonic nanodevices.