Tiller production and survival are suppressed on soils prone to waterlogging. The tiller production and growth of wheat (Triticum aestivum cv. Wyalkatchem) was investigated in a glasshouse experiment during and after a transient waterlogging to examine its effect on grain yield. Wheat plants received either a high or low nitrogen (N) application at sowing and were waterlogged at 22 days after sowing for 14 days. Plants received a second either high or low N application after waterlogging was released. Waterlogging induced a transient N deficiency. The N concentration of the youngest expanded leaf on the mainstem and tillers declined markedly during waterlogging, but its recovery 14 days after the waterlogging was ended was independent of treatment, reaching a greater than the critical minimum concentration of 3.5%. The growth of primary tillers 1 and 2 was severely inhibited by waterlogging while the exsertion of new tillers was delayed by 9 days. Shoot dry weight of the waterlogged plants at final harvest was reduced by 37% compared with the non-waterlogged plants. During the recovery period, the waterlogged plants produced higher order tillers that produced late ears. As a result, the number of ears per plant was similar in plants in continuously drained or previously waterlogged soil. Waterlogging reduced the number of grains per ear on the mainstem and tillers, and consequently grain yield by 32%. High N application after waterlogging increased grain yield by ~20%, but high N applied at sowing had no effect on yield. This suggests that N application after waterlogging can reduce the detrimental effect of waterlogging on grain yields in areas prone to waterlogging.