An experimental investigation of femtosecond laser through-hole drilling of stainless-steel 304 with and without transverse magnetic assistance was conducted. The characteristics of the through-hole geometry and sidewall as well as the chemical composition of the through-hole sidewall surface were analyzed. In addition, a theoretical analysis of magnetic-field-assisted femtosecond laser through-hole drilling is proposed. The results showed that transverse magnetic assistance could improve both the femtosecond laser through-hole drilling quality (through-hole geometry and sidewall characteristics) and efficiency. The primary reason is that transverse magnetic assistance changes the distribution of plasma and reduces the plasma density, which weakens the shielding effect of the plasma. However, compared with nanosecond laser drilling, the effect of the magnetic field on the femtosecond laser through-hole drilling was not obvious. A noticeable thermal effect appeared near the through-hole entrance at a pulse repetition rate of 500 kHz, and a heat affected zone and oxidation zone were produced, which is disadvantageous to laser drilling. This research has good prospects for industrial applications.