The KOI-94 system is a closely-packed, multi-transiting planetary system discovered by the Kepler space telescope. It is known as the first system that exhibited a rare event called a "planet-planet eclipse (PPE)," in which two planets partially overlap with each other in their double-transit phase. In this paper, we constrain the parameters of the KOI-94 system with an analysis of the transit timing variations (TTVs). Such constraints are independent of the radial velocity (RV) analysis recently performed by Weiss and coworkers, and valuable in examining the reliability of the parameter estimate using TTVs. We numerically fit the observed TTVs of KOI-94c, KOI-94d, and KOI-94e for their masses, eccentricities, and longitudes of periastrons, and obtain the best-fit parameters including $m_{\rm c} = 9.4_{-2.1}^{+2.4} M_{⊕}$, $m_{\rm d} = 52.1_{-7.1}^{+6.9} M_{⊕}$, $m_{\rm e} = 13.0_{-2.1}^{+2.5} M_{⊕}$, and $e \lesssim 0.1$ for all the three planets. While these values are mostly in agreement with the RV result, the mass of KOI-94d estimated from the TTV is significantly smaller than the RV value $m_{\rm d} = 106 ± 11 M_{⊕}$. In addition, we find that the TTV of the outermost planet KOI-94e is not well reproduced in the current modeling. We also present analytic modeling of the PPE and derive a simple formula to reconstruct the mutual inclination of the two planets from the observed height, central time, and duration of the brightening caused by the PPE. Based on this model, the implication of the results of TTV analysis for the time of the next PPE is discussed. ; Comment: 18 pages, 17 figures, accepted for publication in ApJ