We present the physical properties of V404 Lyr (KIC 3228863) exhibiting eclipse timing variations and multiperiodic pulsations from all historical data including the ${\it Kepler}$ and SuperWASP observations. Detailed analyses of 2,922 minimum epochs showed that the orbital period has varied through a combination with an upward-opening parabola and two sinusoidal variations, with periods of $P_3$=649 d and $P_4$=2,154 d and semi-amplitudes of $K_3$=193 s and $K_4$=49 s, respectively. The secular period increase with a rate of $+$1.41 $\times 10^{-7}$ d yr$^{-1}$ could be interpreted as a combination of the secondary to primary mass transfer and angular momentum loss. The most reasonable explanation for both sinusoids is a pair of light-travel-time effects due to two circumbinary objects with projected masses of $M_3$=0.47 M$_\odot$ and $M_4$=0.047 M$_\odot$. The third-body parameters are consistent with those calculated using the Wilson-Devinney binary code. For the orbital inclinations $i_4 \ga$ 43$^\circ$, the fourth component has a mass within the hydrogen-burning limit of $\sim$0.07 M$_\odot$, which implies that it is a brown dwarf. A satisfactory model for the {\it Kepler} light curves was obtained through applying a cool spot to the secondary component. The results demonstrate that the close eclipsing pair is in a semi-detached, but near-contact, configuration; the primary fills approximately 93\% of its limiting lobe and is larger than the lobe-filling secondary. Multiple frequency analyses were applied to the light residuals after subtracting the synthetic eclipsing curve from the {\it Kepler} data. This revealed that the primary component of V404 Lyr is a $\gamma$ Dor type pulsating star, exhibiting seven pulsation frequencies in the range of 1.85$-$2.11 d$^{-1}$ with amplitudes of 1.38$-$5.72 mmag and pulsation constants of 0.24$-$0.27 d. The seven frequencies were clearly identified as high-order low-degree gravity-mode oscillations which might be excited through tidal interaction. Only eight eclipsing binaries have been known to contain $\gamma$ Dor pulsating components and, therefore, V404 Lyr will be an important test-bed for investigating these rare and interesting objects.