This study was designed to evaluate the effect of germination time on the proximate composition, functional and pasting properties of flours from red and brown varieties of pigeon pea seeds. The red and brown pigeon pea seeds were cleaned and germinated for 48, 72 and 96 h, respectively and processed into flours, while the flours produced from the ungerminated red and brown pigeon pea seeds served as control samples. The flours obtained were analyzed for proximate, functional and pasting properties using standard methods. The proximate composition of the samples showed that the flours produced from the red pigeon pea seeds had a range of 6.24 – 9.34% moisture, 10.37 – 20.95% crude protein, 1.21 – 1.12% fat, 2.32 – 3.32% ash, 3.14 – 4.23% crude fibre, 76.75-61.07% carbohydrate and 329.29 – 338.10KJ/100g energy, while that of the brown pigeon pea flours had a range of 6.44-9.77% moisture, 10.47-23.69% crude protein, 1.23-1.13% fat, 2.42-3.13% ash, 3.18-4.31% crude fibre, 76.26-57.99% carbohydrate and 358.18-336.83KJ/100g energy. The functional properties of the red pigeon pea flours revealed that the bulk density, water absorption capacity, oil absorption capacity, swelling capacity, gelation capacity and foam capacity ranged from 0.58-022 ml/g, 1.36-1.58 %, 1.40-1.61 %, 2.13-2.38 ml/g, 8.24-11.13 ml/g and 12.28-12.01 %, while that of the brown variety ranged from 0.63-0.36 ml/g, 1.47-1.69 %, 1.46-1.67 %, 1.67-2.46 ml/g, 8.88-11.41 ml/g and 13.33-13.06 %, respectively. The pasting properties of the red pigeon pea flours also showed that the peak, trough, breakdown, set back and final viscosities as well as the peak time and pasting temperature ranged from 3.10 – 5.556cP, 3.35 – 4.86cP, 2.65 – 4.57cP, 5.23 – 7.75cP, 8.82 -10.02cP, 6.79 – 7.34min and 69.79 – 92.710C, while that of the brown variety ranged from 3.59 – 6.21cP, 4.19 – 5.61cP, 3.77 – 5.23cP, 5.59 – 8.25cP, 9.60 – 11.08cP, 7.07 – 7.99min and 80.11 – 99.21oC, respectively. The study, however, revealed that the flours produced from both the red and brown pigeon pea seeds could be generally used as nutrient dense and functional ingredients in the preparation of a wide range of food products especially in Nigeria and other developing countries of the world where there is acute shortage of protein in order to ensure food and nutritional security.