After retiring as a player, Yokoyama took over the coaching reins of Mitsubishi Heavy Industries in 1976, and coached them for eight years, winning the league championship in 1978 and 1982. The team also won the Japan Soccer League Cup twice, in 1978 and 1982, and the Emperor's Cup twice, in 1978 and 1980, making the 1978 season the first domestic treble for a Japanese club.
Following the J. League advent he was called back to the manager's position in 1994 but was unsuccessful and was sacked. In 2000, with Urawa in a second stint in the second tier (the first had been in 1989), Yokoyama was brought back and led them to promotion back to J1 as runner-up.