Fermented dairy products have long been associated with positive health benefits. The present study was undertaken to evaluate the physicochemical and sensory properties, viable probiotic counts, antioxidant activity and total phenolic content of probiotic yoghurt made by reconstituting of whole milk powder in aqueous fennel seed extract. Different concentrations of fennel aqueous seeds extract (2%, 4% and 6% w/v) were used as a substitute for water to reconstitute whole milk powder in formulations of yoghurt as functional additives. Interestingly, the use of aqueous extract of fennel seeds in the reconstituted yoghurt milk did not affect yoghurt composition (moisture, protein, fat and ash contents) compared to plain yoghurt. The titratable acidity significantly decreased after using aqueous fennel seed extract in the yogurt manufacture. In this regard, the titratable acidity value was 0.85 in the control yogurt at the fresh period and 1.14 after 21 days of storage, while this value significantly decreased in the yogurt treatments with 2%, 4% and 6% aqueous fennel seed extract to 80, 0.77 and 0.72, respectively, at fresh period and reached 1.03, 0.96 and 0.94, respectively, after 21 days of storage (p < 0.05). Conversely, the pH values significantly increased (p < 0.05) following the addition of aqueous fennel seed extract in the yogurt manufacture. Moreover, the total phenolic content significantly increased (p < 0.05) from 38.60 (mg GAE/L), in fresh plain yogurt, to 44.80, 53.20 and 64.30 (mg GAE/L), in 2% fennel extract yoghurt (FEY2), 4% fennel extract yoghurt (FEY4) and 6% fennel extract yoghurt (FEY6), respectively. Likewise, the antioxidant activity significantly increased (p < 0.05) from 0.11 (mM TE) in fresh plain yogurt to 0.18, 0.26 and 0.32 (mM TE) in (FEY2), (FEY4) and (FEY6), respectively. The survival of Lactobacillus acidophilus, Streptococcus thermophilus and Bifidobacterium bifidum decreased during storage time in all yoghurt treatments, although it stood at recommended levels for health effects (at least 106 cfu/mL in traditional yoghurt). For sensory evaluation, FEY4 was more acceptable, followed by FEY6, FEY2 and PY, respectively. Collectively, the present study provides useful information about the bioactivity, physicochemical and sensory properties of probiotic yoghurt made from whole milk powder reconstituted in aqueous fennel extract