The 50-year-old was among the top contenders to take over Serbian Raddy Avramovic, who is set to leave his post after next month's AFF Suzuki Cup regardless of how the Lions fare.
But the Singapore legend, who scored 52 goals in 101 games for Singapore, has every intention to honour the two years remaining in his contract with the Johor outfit.
He was quoted as saying by The Straits Times, "I'll be in Johor, I've still got a contract and I'm very happy there. We are now still looking to sign some players."
"I'm still under contract, so I can't discuss other possibilities," he added.
Fandi was part of the Singapore "Dream Team" that took part in the EPL Masters Singapore Cup during the weekend alongside fellow Singapore legends Abbas Saad and current Lions XII coach V. Sundramoorthy, who is also among the favourites to take over the Lions hot seat.