Yep, FIFA (now EA Sports FC) works just fine with a VPN. Plenty of players use one to protect their connection, avoid DDoS attacks, or deal with sketchy networks.
EA's User Agreement doesn't explicitly prohibit the use of VPNs. It does state, however, that you should play fair and not engage in cheating, manipulating, or exploiting the game in any way. So, if you're going to use a VPN, use it fairly.