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Horizon Lines Announces Exchange Offer and Consent Solicitation Extended to October 3, 2011

09.28.2011

CHARLOTTE, NC, September 28, 2011 – Horizon Lines, Inc. (NYSE: HRZ) today announced
that it has extended the expiration date for its previously announced exchange offer and
consent solicitation until 5:00 p.m., New York City time, on October 3, 2011.

The offer is being extended in order to allow sufficient time to address certain important
administrative matters. Additional time is needed for the company to verify the completed
U.S. citizenship questionnaires it has received and to assist noteholders that have tendered
their respective notes in fully completing the required U.S. citizenship questionnaires.

The company intends to complete the exchange offer of the existing 4.25% Convertible
Senior Notes due 2012 (the “2012 convertible notes”) on or before October 6, 2011, at
which time it expects to close the entire refinancing.

The exchange offer and consent solicitation had been scheduled to expire at 5:00 p.m., New
York City time, on September 27, 2011. As of the prior expiration date on September 27,
2011, 99.3% of the $330.0 million aggregate principal amount of the 2012 convertible
notes had been tendered into the exchange offer and consent solicitation.

As part of the exchange offer, the company is also seeking consents from all holders of the
existing 2012 convertible notes to remove substantially all of the restrictive covenants and
certain events of default from the indenture governing the 2012 convertible notes.

The company and its advisors continue to work with the financial and legal advisors to the
informal committee of noteholders to finalize the documentation and terms of the
recapitalization plan, of which the exchange offer and consent solicitation are an integral
part.

Important Information About the Exchange Offer

This press release is for informational purposes only and is not an offer to buy or the
solicitation of an offer to sell any security. The exchange offer is only being made by means
of a prospectus, a letter of transmittal and other offer documents, as described below.

In connection with the exchange offer by Horizon Lines, Inc., the company previously filed a
Registration Statement on Form S-4 (which contains a preliminary prospectus),
amendments to the Registration Statement, an exchange offer statement on Schedule TO, as
amended, and other related documents and materials with the SEC. Investors and security
holders are strongly urged to carefully review the Registration Statement, amendments to
the Registration Statement, the preliminary prospectus, the exchange offer statement, the
amendments to the exchange offer statement and the other related documents and
materials filed with the SEC, including the final prospectus described below, when
available, as well as any amendments and supplements thereto, because they will contain
important information about the company, the exchange offer and related transactions and
are the sole means by which any offer to exchange or sell, or any solicitation of any such
offers, will be made.

The preliminary prospectus, the prospectus supplements and related transmittal materials
have been delivered to holders of the 2012 convertible notes. Investors and security
holders may obtain a free copy of the registration statement, amendments to the
registration statement, preliminary prospectus, the prospectus supplements and
transmittal materials, as well as other documents filed by the company with the SEC, at the
SEC’s website, www.sec.gov. Prior to the completion of the exchange offer, the registration
statement must become effective under the securities laws, and after effectiveness, the
company will file a final prospectus with the SEC. Investors and security holders are
strongly urged to carefully review the final prospectus when it is available. Copies of the
exchange offer documents and other filed documents will be available for free at the
company’s website, www.horizonlines.com, or by making a request to Horizon Lines, Inc.,
4064 Colony Road, Suite 200, Charlotte, North Carolina 28211, (704) 973-7000, Attention:
Jim Storey, Director, Investor Relations & Corporate Communications.

About Horizon Lines

Horizon Lines, Inc. is the nation’s leading domestic ocean shipping and integrated logistics
company. The company owns or leases a fleet of 20 U.S.-flag containerships and operates
five port terminals linking the continental United States with Alaska, Hawaii, Guam,
Micronesia and Puerto Rico. The company provides express trans-Pacific service between
the U.S. West Coast and the ports of Ningbo and Shanghai in China, manages a domestic and
overseas service partner network and provides integrated, reliable and cost competitive
logistics solutions. Horizon Lines, Inc., is based in Charlotte, NC, and trades on the New
York Stock Exchange under the ticker symbol HRZ.

Forward Looking Statements

The information contained in this press release should be read in conjunction with our
filings made with the Securities and Exchange Commission. This press release contains
“forward-looking statements” within the meaning of the federal securities laws. Forwardlooking
statements are those that do not relate solely to historical fact. They include, but
are not limited to, any statement that may predict, forecast, indicate or imply future results,
performance, achievements or events. Words such as, but not limited to, “will,” “intend,”
“expect,” “would,” “could,” “must,” “may,” and similar expressions or phrases identify
forward-looking statements.

Factors that may cause expected results or anticipated events or circumstances discussed
in this press release to not occur or to differ from expected results include: the ability of the
parties to agree on the final terms of the refinancing; our ability to close on the refinancing;
our ability to satisfy other conditions of the refinancing, including satisfaction of any
remaining diligence requests; the ability of the investors to fund the refinancing; general
conditions in the capital markets; general economic conditions; our ability to maintain
adequate liquidity to operate our business; volatility in fuel prices and in freight rates;
decreases in shipping volumes; our ability to remain Jones Act compliant because of
changes in ownership; or our ability to continue as a going concern.

All forward-looking statements involve risk and uncertainties. In light of these risks and
uncertainties, expected results or other anticipated events or circumstances discussed in
this press release might not occur. The forward-looking statements included in the press
release are made only as of the date they are made and the company undertakes no
obligation to update any such statements, except as otherwise required by applicable law.
See the section entitled “Risk Factors” in our Form 10-K filed with the SEC on March 28,
2011, for a more complete discussion of these risks and uncertainties and for other risks
and uncertainties. Those factors and the other risk factors described therein are not
necessarily all of the important factors that could cause actual results or developments to
differ materially from those expressed in any of our forward-looking statements. Other
unknown or unpredictable factors also could harm our results. Consequently, there can be
no assurance that actual results or developments anticipated by us will be realized or, even
if substantially realized, that they will have the expected consequences.

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