The 1998–99 Cypriot Second Division was the 44th season of the Cypriot second-level football league. Anagennisi Deryneia won their 1st title.

Fourteen teams participated in the 1998–99 Cypriot Second Division. All teams played against each other twice, once at their home and once away. The team with the most points at the end of the season crowned champions. The first three teams were promoted to 1999–2000 Cypriot First Division and the last three teams were relegated to the 1999–2000 Cypriot Third Division.

Teams promoted to 1998–99 Cypriot First Division

• Olympiakos Nicosia
• Aris Limassol
• Doxa Katokopias

Teams relegated from 1997–98 Cypriot First Division

• Anagennisi Deryneia
• APOP Paphos
• Ethnikos Assia

Teams promoted from 1997–98 Cypriot Third Division

• AEZ Zakakiou
• AEK/Achilleas Ayiou Theraponta
• Anagennisi Germasogeias

Teams relegated to 1998–99 Cypriot Third Division

• Chalkanoras Idaliou
• Iraklis Gerolakkou
• APEP

• Cypriot Second Division
• 1998–99 Cypriot First Division
• 1998–99 Cypriot Cup

• "1998/99 Cypriot Second Division". Rec.Sport.Soccer Statistics Foundation. 2016-01-14. Retrieved 2016-01-14.

v t e Cypriot Second Division
2023–24 clubs	Achyronas-Onisilos Akritas ASIL Ayia Napa Digenis Morphou ENAD ENP Ermis Aradippou Krasava MEAP Olympiakos Omonia 29M Omonia Ar. PAEEK Peyia P.O. Xylotymbou
Associated competitions	First Division Third Division STOK Elite Division Women's 1st Division Cypriot Women's Cup Cypriot Women's Super Cup Cypriot Cup Cypriot Super Cup
Seasons	1953–54 1954–55 1955–56 1956–57 1957–58 1958–59 1959–60 1960–61 1961–62 1962–63 1963–64 1964–65 1965–66 1966–67 1967–68 1968–69 1969–70 1970–71 1971–72 1972–73 1973–74 1974–75 1975–76 1976–77 1977–78 1978–79 1979–80 1980–81 1981–82 1982–83 1983–84 1984–85 1985–86 1986–87 1987–88 1988–89 1989–90 1990–91 1991–92 1992–93 1993–94 1994–95 1995–96 1996–97 1997–98 1998–99 1999–00 2000–01 2001–02 2002–03 2003–04 2004–05 2005–06 2006–07 2007–08 2008–09 2009–10 2010–11 2011–12 2012–13 2013–14 2014–15 2015–16 2016–17 2017–18 2018–19 2019–20 2020–21 2021–22 2022–23 2023–24