This study tested for association between Toxoplasma gondii and pregnancy and abortion to investigate sub-optimal reproduction in farmed red deer (Cervus elaphus). Sera from a sub-sample (n = 2304) of pregnant and non-pregnant hinds in early gestation at first pregnancy scan (scan 1) and approximately at the end of second trimester at second pregnancy scan (scan 2) were tested for T. gondii antibodies using a validated ELISA. Foetuses and/or uteri from pregnant, non-pregnant, and aborting hinds at scan 1, scan 2, or weaning were tested for T. gondii DNA by nested PCR. At scan 1, 31.1% of 861 rising two-year-old (R2) and 28.3% of 357 mixed-aged (MA, ≥ 2 years) hinds were sero-positive. There was no association between scan 1 serology and non-pregnancy at animal (R2, p = 0.05 and MA, p = 0.43) or herd level (R2, p = 0.37). Toxoplasma gondii DNA was detected in 3/18 placenta and 4/18 foetal brains from aborting R2 hinds and 15/157 R2 and 3/21 MA uteri from non-pregnant hinds at scan 1. At scan 2, sero-prevalence was higher (odds ratio = 1.6, 95% CI = 1.04-2.48) in aborted (34.3% of 268) than in non-aborted (23.5% of 446) R2 hinds (p = 0.03) and 7.9% of abortions between scans were attributable to T. gondii exposure. Within-herd sero-prevalence at scan 2 was positively associated with daily abortion rate in R2 herds with aborted hinds (p < 0.001) but not in MA herds (p = 0.07). Toxoplasma gondii DNA was detected in 27/169 uteri, 2/20 cotyledons, and 1/5 foetal brains from aborted hinds at scan 2 and in uteri from 5/33 hinds not rearing a calf to weaning. Toxoplasma gondii RFLP genotyping of five loci revealed a unique type I/III genotype pattern, TgRDNZ1, in a foetal brain sample, not been previously reported in deer. These findings provide serological and molecular evidence that T. gondii infection is associated with abortion in red deer, possibly in all three trimesters.