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(1) Background: Wild cervids play an important role in transmission cycles of tick-borne pathogens; however, investigations of tick-borne pathogens in sika deer in Germany are lacking. (2) Methods: Spleen tissue of 74 sympatric wild cervids (30 roe deer, 7 fallow deer, 22 sika deer, 15 red deer) and of 27 red deer from a farm from southeastern Germany were analyzed by molecular methods for the presence of <i>Anaplasma phagocytophilum</i> and <i>Babesia</i> species. (3) Results: <i>Anaplasma phagocytophilum</i> and <i>Babesia</i> DNA was demonstrated in 90.5% and 47.3% of the 74 combined wild cervids and 14.8% and 18.5% of the farmed deer, respectively. Twelve <i>16S rRNA</i> variants of <i>A. phagocytophilum</i> were delineated. While the infection rate for <i>A. phagocytophilum</i> among the four cervid species was similar (71.4% to 100%), it varied significantly for <i>Babesia</i> between roe deer (73.3%), fallow deer (14.3%), sika deer (27.3%) and red deer (40.0%). Deer ≤2 years of age tested significantly more often positive than the older deer for both <i>A. phagocytophilum</i> and <i>Babesia</i> species. (4) Conclusions: This study confirms the widespread occurrence of <i>A. phagocytophilum</i> and <i>Babesia</i> species in wild cervids and farmed red deer in Germany and documents the co-occurrence of the two tick-borne pathogens in free-ranging sika deer.