A series of YAG:Ce,Mn transparent ceramics were prepared via a solid-state reaction-vacuum sintering method. The effects of various Mn²⁺–Si⁴⁺ pair doping levels on the structure, transmittance, and luminescence properties were systematically investigated. These transparent ceramics have average grain sizes of 10–16 μm, clean grain boundaries, and excellent transmittance up to 83.4% at 800 nm. Under the excitation of 460 nm, three obvious emission peaks appear at 533, 590, and 745 nm, which can be assigned to the transition 5d→4f of Ce³⁺ and ⁴T₁→⁶A₁ of Mn²⁺. Thus, the Mn²⁺–Si⁴⁺ pairs can effectively modulate the emission spectrum by compensating broad orange-red and red spectrum component to yield high quality warm white light. After the optimized YAG:Ce,Mn transparent ceramic packaged with blue light-emitting diode (LED) chips, correlated color temperature (CCT) as low as 3723 K and luminous efficiency (LE) as high as 96.54 lm/W were achieved, implying a very promising candidate for application in white light-emitting diodes (WLEDs) industry.