Season 3 of Codename: Kids Next Door premiered on June 11, 2004 on the Cartoon Network in the United States. It ran up through November 12, 2004. Season 3 has thirteen episodes. Ten of them are made up of two eleven-minute episodes. The other three are full length episodes, each of them being twenty-two minutes long. This season, like its predecessor, reveals more about the KND Global Command and Moonbase Headquarters, all while still focusing mostly on Sector V.
Episodes
| E# | Code | Mission A | Mission B | Original Airdate |
| 27 | 301 | Operation: F.U.T.U.R.E. | June 11, 2004 | |
| 28 | 302 | Operation: A.F.L.O.A.T. | Operation: L.E.A.D.E.R. | June 18, 2004 |
| 29 | 303 | Operation: U.T.O.P.I.A. | Operation: R.O.B.B.E.R.S. | June 25, 2004 |
| 30 | 304 | Operation: F.O.U.N.T.A.I.N. | July 9, 2004 | |
| 31 | 305 | Operation: B.U.T.T. | Operation: T.R.A.I.N.I.N.G. | July 16, 2004 |
| 32 | 306 | Operation: A.R.C.H.I.V.E. | Operation: S.L.U.M.B.E.R. | July 23, 2004 |
| 33 | 307 | Operation: P.I.N.K.-E.Y.E. | Operation: K.A.S.T.L.E. | July 30, 2004 |
| 34 | 308 | Operation: C.A.K.E.D.-T.H.R.E.E. | Operation: L.O.C.K.D.O.W.N. | August 6, 2004 |
| 35 | 309 | Operation: H.U.G.S. | Operation: J.E.W.E.L.S. | August 13, 2004 |
| 36 | 310 | Operation: G.R.A.D.U.A.T.E.S. | August 6, 2004 | |
| 37 | 311 | Operation: T.R.I.C.K.Y. | Operation: U.N.C.O.O.L. | October 29, 2004 |
| 38 | 312 | Operation: P.R.E.S.I.D.E.N.T. | Operation: H.O.S.P.I.T.A.L. | November 5, 2004 |
| 39 | 313 | Operation: S.P.R.O.U.T. | Operation: H.O.U.N.D. | November 12, 2004 |
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Season 3 | Next Season S4 |