Abstract The Neptunian satellite system is unusual, comprising Triton, a large (∼2700 km) moon on a close-in, circular, yet retrograde orbit, flanked by Nereid, the largest irregular satellite (∼300 km) on a highly eccentric orbit. Capture origins have been previously suggested for both moons. Here we explore an alternative in situ formation model where the two satellites accreted in the circum-Neptunian disk and are imparted irregular and eccentric orbits by a deep planetary encounter with an ice giant (IG), like that predicted in the Nice scenario of early solar system development. We use N-body simulations of an IG approaching Neptune to 20 Neptunian radii (R Nep), through a belt of circular prograde regular satellites at 10–30 R Nep. We find that half of these primordial satellites remain bound to Neptune and that 0.4%–3% are scattered directly onto wide and eccentric orbits resembling that of Nereid. With better matches to the observed orbit, our model has a success rate comparable to or higher than capture of large Nereid-sized irregular satellites from heliocentric orbit. At the same time, the IG encounter injects a large primordial moon onto a retrograde orbit with specific angular momentum similar to Triton’s in 0.3%–3% of our runs. While less efficient than capture scenarios, our model does indicate that an in situ origin for Triton is dynamically possible. We also simulate the post-encounter collisional and tidal orbital evolution of Triton analog satellites and find they are decoupled from Nereid on timescales of ∼104 yr, in agreement with Cuk & Gladman.